Bowtie2
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Available modules
The overview below shows which Bowtie2 installations are available per target architecture in the HPCC module system, ordered based on software version (new to old).
To start using Bowtie2, load one of these modules using a module load command like:
1 | |
(This data was automatically generated on Thu, 08 May 2025 at 12:07:26 EDT)
| neoverse_v1 | generic | zen2 | zen3 | zen4 | haswell | skylake_avx512 | |
|---|---|---|---|---|---|---|---|
| Grace Nodes | everywhere (except Grace nodes) | amd20 | amd22 | amd24 | intel16 | intel18,amd20-v100,amd21,intel21 | |
| Bowtie2/2.5.1-GCC-12.3.0 | - | x | - | - | - | - | - |
| Bowtie2/2.5.1-GCC-12.2.0 | - | x | - | - | - | - | - |
| Bowtie2/2.4.5-GCC-11.3.0 | - | - | - | - | - | x | - |