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
# 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