MetaCompass
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marbl
marbl
MetaCompass: Reference-guided Assembly of Metagenomes
MetaCompass v2.0-beta
Last updated: January 31th, 2021
Publication
Victoria Cepeda, Bo Liu, Mathieu Almeida, Christopher M. Hill, Sergey Koren, Todd J. Treangen, Mihai Pop. bioRxiv 212506; doi: https://doi.org/10.1101/212506
Required software:
- Python3 (>=) 3.1: https://www.python.org/download/releases/3.0/
- BioPython: https://biopython.org/
- snakemake (>=) v3.7.1: https://snakemake.readthedocs.io/en/stable/getting_started/installation.html
- BLAST+ (>=) 2.4.0: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST
- bowtie2 (>=) 2.2.9: https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9
- kmer-mask (May 13th, 2015): https://sourceforge.net/projects/kmer/files/meryl-r2013.tar.xz
- mash (>=) 2.1: https://github.com/marbl/Mash/releases/tag/v2.1
- samtools (>=) 1.x: http://samtools.sourceforge.net/
- MEGAHIT (>=) 1.0.6: https://github.com/voutcn/megahit
- ntHits: https://github.com/bcgsc/ntHits
- ntEdit: https://github.com/bcgsc/ntedit
Memory and Disk Space Requirements.
- 90GB or more hard disk space to perform a normal installation.
- 8GB or more memory.
INSTALLATION From Source:
Get the Latest release from https://github.com/marbl/MetaCompass/releases:
wget https://github.com/marbl/MetaCompass/archive/1.xx.tar.gz
tar -xzvf 1.xx.tar.gz
cd MetaCompass-1.xx
./install.sh
INSTALLATION Using Git:
git clone https://github.com/marbl/MetaCompass.git
cd MetaCompass
./install.sh
USAGE
-- I have a set of metagenomic reads, and want to perform reference-guided assembly.
python3 go_metacompass.py -1 [read1.fq] -2 [read2.fq] -l [max read length] -o [output_folder] -m [min coverage] -t [ncpu] -y [memory GB]
-- I know the reference genomes, or I want to perform comparative assembly for a particular genome.
python3 go_metacompass.py -r [references.fasta] -1 [read1.fq] -2 [read2.fq] -o [output_folder] -m [min coverage] -t [ncpu] -y [memory GB]
OUTPUT
-- metacompass_output folder contains the following files:
| File | Description |
|---|---|
| metacompass.final.ctg.fa | Assembled contigs |
| metacompass_mapping_stats.tsv | Mapped reads general stats |
| metacompass_mapping_pergenome_stats.tsv | Mapped reads stats per genome |
| metacompass.genomes_coverage.txt | Breadth of coverage per genome |
| metacompass.references.fna | References used to guide assembly |
| metacompass_assembly_stats.tsv | Assembly general stats |
| metacompass_assembly_pergenome_stats | Assembly stats per genome |
| metacompass_summary.tsv | Metadata |
EXAMPLES
Reference-guided assembly with known reference genomes (no reference selection).
-- Input data is available in the tutorial folder:
Reference genome file: Candidatus_Carsonella_ruddii_HT_Thao2000.fasta
Metagenomic reads: thao2000.1.fq
thao2000.2.fq
-- Run:
python3 go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -1 tutorial/thao2000.1.fq -2 tutorial/thao2000.2.fq -l 150 -o example1_output -t 4 -y 8
Reference-guided assembly with reference selection.
-- Download and extract metagenomic sample:
wget http://downloads.hmpdacc.org/dacc/hhs/genome/microbiome/wgs/analysis/hmwgsqc/v2/SRS044742.tar.bz2
tar -xvf SRS044742.tar.bz2
-- The metagenomic sample contains:
SRS044742/
SRS044742.denovo_duplicates_marked.trimmed.1.fastq
SRS044742.denovo_duplicates_marked.trimmed.2.fastq
SRS044742.denovo_duplicates_marked.trimmed.singleton.fastq
-- Run:
python3 go_metacompass.py -1 SRS044742/SRS044742.denovo_duplicates_marked.trimmed.1.fastq -2 SRS044742/SRS044742.denovo_duplicates_marked.trimmed.2.fastq -U SRS044742/SRS044742.denovo_duplicates_marked.trimmed.singleton.fastq -l 100 -o example2_output -t 1 -y 8
Contact: [email protected]
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