bioconvert

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Bioconvert ##########

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

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:contributions: Want to add a convertor ? Please join https://github.com/bioconvert/bioconvert/issues/1 :issues: Please use https://github.com/bioconvert/bioconvert/issues

Overview ########

Life science uses many different formats. They may be old, or with complex syntax and converting those formats may be a challenge. Bioconvert aims at providing a common tool / interface to convert life science data formats from one to another.

Many conversion tools already exist but they may be dispersed, focused on few specific formats, difficult to install, or not optimised. With Bioconvert, we plan to cover a wide spectrum of format conversions; we will re-use existing tools when possible and provide facilities to compare different conversion tools or methods via benchmarking. New implementations are provided when considered better than existing ones.

In March 2022, we had 48 formats, 98 direct conversions (125 different methods).

.. image:: https://raw.githubusercontent.com/bioconvert/bioconvert/main/doc/conversion.png :width: 80%

Installation ###############

In order to install bioconvert, you can use pip::

pip install bioconvert

We also provide releases on bioconda (http://bioconda.github.io/)::

conda install bioconvert

and Singularity containers are available. See http://bioconvert.readthedocs.io/en/main/user_guide.html#installation for details.

bioconvert is a Python library but depends on many third-party software (e.g., samtools). Therefore, the bioconda method is the recommended one for end-users because it installs bioconvert and all its dependencies. If you choose the pip method, only the bioconvert Python package will be installed.

Usage ##########

From the command line, you can convert a FastQ file into a FastA file as follows (compressed or not)::

bioconvert fastq2fasta input.fastq output.fasta
bioconvert fastq2fasta input.fq    output.fasta
bioconvert fastq2fasta input.fq.gz output.fasta.gz
bioconvert fastq2fasta input.fq.gz output.fasta.bz2

When there is no ambiguity, you can be implicit::

 bioconvert input.fastq output.fasta

For help, just type::

bioconvert --help
bioconvert fastq2fasta --help

From a Python shell::

# import a converter
from bioconvert.fastq2fasta import FASTQ2FASTA

# Instanciate with infile/outfile names
convert = FASTQ2FASTA(infile, outfile)

# the conversion itself
convert()

Available Converters #######################

.. list-table:: Conversion table :widths: 20 40 40 :header-rows: 1

* - Converters
  - CI testing
  - Default method
* - `abi2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.abi2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/abi2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/abi2fasta.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `abi2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.abi2fastq>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/abi2fastq.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/abi2fastq.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `abi2qual <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.abi2qual>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/abi2qual.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/abi2qual.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2bedgraph <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2bedgraph>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2bedgraph.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2bedgraph.yml
  - `BEDTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2bigwig <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2bigwig>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2bigwig.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2bigwig.yml
  -
* - `bam2cov <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2cov>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2cov.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2cov.yml
  - `BEDTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2cram <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2cram>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2cram.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2cram.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2fasta.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2fastq>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2fastq.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2fastq.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2json <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2json>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2json.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2json.yml
  - `BAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2sam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2sam>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2sam.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2sam.yml
  - `SAMBAMBA <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2tsv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2tsv>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2tsv.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2tsv.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2wiggle>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2wiggle.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2wiggle.yml
  - `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bcf2vcf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bcf2vcf>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bcf2vcf.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bcf2vcf.yml
  - `BCFTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bcf2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bcf2wiggle>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bcf2wiggle.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bcf2wiggle.yml
  - `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bed2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bed2wiggle>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bed2wiggle.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bed2wiggle.yml
  - `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bedgraph2bigwig <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bedgraph2bigwig>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2bigwig.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2bigwig.yml
  - `UCSC <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bedgraph2cov <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bedgraph2cov>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2cov.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2cov.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bedgraph2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bedgraph2wiggle>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2wiggle.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2wiggle.yml
  - `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bigbed2bed <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bigbed2bed>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bigbed2bed.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bigbed2bed.yml
  - `DEEPTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bigbed2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bigbed2wiggle>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bigbed2wiggle.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bigbed2wiggle.yml
  - `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bigwig2bedgraph <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bigwig2bedgraph>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bigwig2bedgraph.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bigwig2bedgraph.yml
  - `DEEPTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bigwig2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bigwig2wiggle>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bigwig2wiggle.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bigwig2wiggle.yml
  - `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bplink2plink <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bplink2plink>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bplink2plink.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bplink2plink.yml
  - `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bplink2vcf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bplink2vcf>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bplink2vcf.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bplink2vcf.yml
  - `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bz22gz <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bz22gz>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bz22gz.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/bz22gz.yml
  - Unix commands
* - `clustal2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.clustal2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2fasta.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `clustal2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.clustal2nexus>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2nexus.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2nexus.yml
  - `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `clustal2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.clustal2phylip>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2phylip.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2phylip.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `clustal2stockholm <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.clustal2stockholm>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2stockholm.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2stockholm.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `cram2bam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.cram2bam>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/cram2bam.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/cram2bam.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `cram2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.cram2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/cram2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/cram2fasta.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `cram2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.cram2fastq>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/cram2fastq.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/cram2fastq.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `cram2sam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.cram2sam>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/cram2sam.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/cram2sam.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `csv2tsv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.csv2tsv>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/csv2tsv.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/csv2tsv.yml
  -
* - `csv2xls <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.csv2xls>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/csv2xls.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/csv2xls.yml
  -
* - `dsrc2gz <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.dsrc2gz>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/dsrc2gz.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/dsrc2gz.yml
  -
* - `embl2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.embl2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/embl2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/embl2fasta.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `embl2genbank <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.embl2genbank>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/embl2genbank.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/embl2genbank.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2clustal <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2clustal>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2clustal.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2clustal.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2faa <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2faa>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2faa.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2faa.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2fasta_agp <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2fasta_agp>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2fasta_agp.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2fasta_agp.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2fastq>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2fastq.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2fastq.yml
  - `PYSAM <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2genbank <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2genbank>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2genbank.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2genbank.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2nexus>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2nexus.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2nexus.yml
  - `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2phylip>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2phylip.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2phylip.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2twobit <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2twobit>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2twobit.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2twobit.yml
  - `UCSC <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta_qual2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta_qual2fastq>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta_qual2fastq.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta_qual2fastq.yml
  - `PYSAM <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fastq2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fastq2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2fasta.yml
  -  `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_  `available <_static/benchmark_fastq2fasta.png>`_
* - `fastq2fasta_qual <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fastq2fasta_qual>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2fasta_qual.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2fasta_qual.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fastq2qual <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fastq2qual>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2qual.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2qual.yml
  - `READFQ <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `genbank2embl <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.genbank2embl>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2embl.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2embl.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `genbank2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.genbank2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2fasta.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `genbank2gff3 <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.genbank2gff3>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2gff3.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2gff3.yml
  - `BIOCODE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gfa2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gfa2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gfa2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/gfa2fasta.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gff22gff3 <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gff22gff3>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gff22gff3.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/gff22gff3.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gff32gff2 <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gff32gff2>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gff32gff2.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/gff32gff2.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gff32gtf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gff32gtf>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gff32gtf.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/gff32gtf.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gz2bz2 <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gz2bz2>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gz2bz2.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/gz2bz2.yml
  -
* - `gz2dsrc <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gz2dsrc>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gz2dsrc.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/gz2dsrc.yml
  -
* - `json2yaml <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.json2yaml>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/json2yaml.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/json2yaml.yml
  -
* - `maf2sam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.maf2sam>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/maf2sam.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/maf2sam.yml
  - ?
* - `newick2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.newick2nexus>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/newick2nexus.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/newick2nexus.yml
  - `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `newick2phyloxml <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.newick2phyloxml>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/newick2phyloxml.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/newick2phyloxml.yml
  - `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2clustal <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2clustal>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2clustal.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2clustal.yml
  - `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2fasta.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2newick <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2newick>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2newick.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2newick.yml
  - `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2phylip>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2phylip.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2phylip.yml
  - `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2phyloxml <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2phyloxml>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2phyloxml.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2phyloxml.yml
  - `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `ods2csv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.ods2csv>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/ods2csv.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/ods2csv.yml
  -
* - `phylip2clustal <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2clustal>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2clustal.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2clustal.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phylip2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2fasta.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phylip2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2nexus>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2nexus.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2nexus.yml
  - `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phylip2stockholm <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2stockholm>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2stockholm.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2stockholm.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phylip2xmfa <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2xmfa>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2xmfa.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2xmfa.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phyloxml2newick <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phyloxml2newick>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phyloxml2newick.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/phyloxml2newick.yml
  - `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phyloxml2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phyloxml2nexus>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phyloxml2nexus.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/phyloxml2nexus.yml
  - `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `plink2bplink <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.plink2bplink>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/plink2bplink.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/plink2bplink.yml
  - `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `plink2vcf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.plink2vcf>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/plink2vcf.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/plink2vcf.yml
  - `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `sam2bam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.sam2bam>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/sam2bam.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/sam2bam.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `sam2cram <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.sam2cram>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/sam2cram.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/sam2cram.yml
  - `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `sam2paf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.sam2paf>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/sam2paf.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/sam2paf.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `scf2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.scf2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/scf2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/scf2fasta.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `scf2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.scf2fastq>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/scf2fastq.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/scf2fastq.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `sra2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.sra2fastq>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/sra2fastq.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/sra2fastq.yml
  - `FASTQDUMP <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `stockholm2clustal <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.stockholm2clustal>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/stockholm2clustal.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/stockholm2clustal.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `stockholm2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.stockholm2phylip>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/stockholm2phylip.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/stockholm2phylip.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `tsv2csv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.tsv2csv>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/tsv2csv.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/tsv2csv.yml
  -
* - `twobit2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.twobit2fasta>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/twobit2fasta.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/twobit2fasta.yml
  - `DEEPTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2bcf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2bcf>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bcf.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bcf.yml
  - `BCFTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2bed <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2bed>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bed.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bed.yml
  - `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2bplink <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2bplink>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bplink.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bplink.yml
  - `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2plink <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2plink>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2plink.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2plink.yml
  - `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2wiggle>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2wiggle.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2wiggle.yml
  - `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `wig2bed <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.wig2bed>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/wig2bed.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/wig2bed.yml
  - `BEDOPS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `xls2csv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.xls2csv>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/xls2csv.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/xls2csv.yml
  -
* - `xlsx2csv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.xlsx2csv>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/xlsx2csv.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/xlsx2csv.yml
  -
* - `xmfa2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.xmfa2phylip>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/xmfa2phylip.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/xmfa2phylip.yml
  - `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `yaml2json <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.yaml2json>`_
  - .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/yaml2json.yml/badge.svg
        :target: https://github.com/bioconvert/bioconvert/actions/workflows/yaml2json.yml
  -

Contributors ############

Setting up and maintaining Bioconvert has been possible thanks to users and contributors. Thanks to all:

.. image:: https://contrib.rocks/image?repo=bioconvert/bioconvert :target: https://github.com/bioconvert/bioconvert/graphs/contributors

Changes ########

========= ============================================================================== Version Description ========= ============================================================================== 0.6.2 * added gff3 to gtf conversion 0.6.1 * output file can be in sub-directories allowing syntax such as 'bioconvert fastq2fasta test.fastq outputs/test.fasta * fix all CI actions * add more examples as notebooks in ./examples * add a Snakefile for the paper in ./doc/Snakefile_paper 0.6.0 * Fix bug in bam2sam (method sambamba) * Fix graph layout * add threading in fastq2fasta (seqkit method) * multibenchmark feature added * stable version used for web interface 0.5.2 * Update requirements and environment.yml and add a conda spec-file.txt file 0.5.1 * add genbank2gff3 requirement material in bioconvert.utils.biocode 0.5.0 * Add CI actions for all converters * remove sniffer (now in biosniff on pypi https://pypi.org/project/biosniff/) * A complete benchmarking suite (see doc/Snakefile_benchmark file and benchmarking) * documentation and tests for all converters * removed the validators (we assume intputs are correct) ========= ==============================================================================