Bowtie2

Bowtie2 is a tool for aligning sequencing reads to long genomes. It indexes the reference genome using FM indexing and then aligns the reads. The resulting alignments are output in the SAM format. By default these alignments are end-to-end, but they can be set to local. In local mode Bowtie2 will trim some read characters on either end to maximize alignment score. Two additional tools are loaded with Bowtie2: bowtie2-build and bowtie2-inspect.

When searching for alignments, Bowtie2 looks for concordant and discordant alignments, meaning those where the pairs align in the expected orientation within expected ranges as well as those that do not. Additionally, it does NOT guarantee that the alignment reported is the best possible in the terms of alignment score. In the event that two alignments are identical it uses a pseudo-random number to choose.

For additional information and examples, please see the Bowtie2 documentation.

ml biocontainers bowtie2
# for unpaired reads
bowtie2 -x <basename of the index for reference genome> -u longreads.fq
# for paired reads
bowtie2 -x <basename of the index for reference genome> -1 forward_reads.fq -2 reverse_reads.fq

Parallel Capabilities: Single core default, multithreading options supported.