1.20.c

htslib container

Main tool: htslib

Code repository: https://github.com/samtools/htslib

Additional tools:

• perl 5.34.0

Basic information on how to use this tool:

• executable: htsfile
• help: --help
• version: --version
• description: The htsfile utility attempts to identify what kind of high-throughput sequencing data files the specified files are, and provides minimal viewing capabilities for some kinds of data file.

Additional information:

This container includes htslib v1.20 compiled with libdeflate for a better cloud performance.

Full documentation: https://www.htslib.org/doc/samtools.html

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