Subread

Subread acts as a general alignment tool which can align both genomic DNA and RNA-sequencing reads. It can also discover genomic mutations such as indels and structural variants. When multithreading, max threads useable is 32.

tip

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

report_subtools.sh subread

For additional information and examples, please see the Subread documentation.

ml biocontainers subread
subread-buildindex -o <index name> <list of ref.fa>
subread-align -i <index name> -r <reads.txt.gz> -o <results.bam>

Parallel Capabilities: Single core default, multithreading options supported.