HTSeq

HTSeq is for high throughput sequencing data analysis. Covering everything from BAM file manipulation to counting reads, this package is a helpful tool for sequence analysis. This module consists of htseq-count, htseq-count-barcodes, and htseq-qa. htseq-count accepts a list of alignment files and a gff file for input while outputting a counts file. htseq-count-barcodes is similar to htseq-count but is designed for SAM, BAM, and CRAM file formats.

For additional information and examples, please refer to the HTSeq documentation.

Execution:

ml biocontainers htseq
htseq-count <alignment files> <gff file>

tip

Several other tools load with this module. Review additional available tools using the command below:

report_subtools.sh htseq

Parallel Capabilities: Single core default, multithreading options supported.