README.md

htslib container

Main tool:

• https://www.htslib.org/
• GitHub

Additional tools:

• perl 5.30.0

Example Usage

# determine file formats for various BAM and SAM files
$ htsfile tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam 
tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam:     BAM version 1 compressed sequence data

$ htsfile ce_tag_padded.sam
ce_tag_padded.sam:      SAM version 1.4 sequence text

# compresses sample.fastq to sample.fastq.gz in BGZF format (blocked GNU Zip Format)
$ bgzip sample.fastq

Better documentation can be found at https://www.htslib.org/doc/samtools.html