viral-ngs
viral-ngs copied to clipboard
broadinstitute
Viral genomics analysis pipelines
All throughout the pipeline, there are places that assume paired-end reads, and it's mostly how we wrap underlying tools, probably not the underlying tools themselves. For example, BAM->fastq conversion for...
Apparently Illumina uses the Q=2 quality score as a "Read Segment Quality Control Indicator". I can't find any recent mentions of this on Illumina's website. One document from 2011 describes...
Similar to how we write a spikein report, we should consider adding a report on insert sizes via Picard's `CollectInsertSizeMetrics`.
Our pipeline currently has a gate to only consider assemblies successful if their length is greater than `assembly_min_length_fraction_of_reference`. In our metrics we report the assembly length (if it passes), but...
Hi, Reported this error when using deplete_blastn_paired. > BLAST Database error: No alias or index file found for nucleotide database [xxxx.fasta] in search path Does anyone know why? Thanks!
With #356, the VCF file created by `intrahost.py`'s `merge_to_vcf` reports read depth, at a given position, only for samples that contain alternate alleles at that position. If a sample has...
We should expand the documentation to include mention of how to start with demultiplexing in the Snakemake pipeline, on the Broad cluster or elsewhere, where the barcode files list paths...
It looks like it is now generally available and default: travis-ci/travis-ci#2320
pysam mostly works with Travis, except a few of the functions that embed samtools functionality (like pysam.view) which do some weird redirection of stdin/stdout, but Travis does some weird redirection...
Create a script that merges BAM files of unaligned reads together while also presenting the opportunity to rewrite certain bits of commonly rewritten metadata, like the sample name and library...