RESEARCH USE
Where Bowtie 2 fits
Bowtie 2 builds an FM index for a reference and aligns single-end or paired-end reads in end-to-end or local mode, producing SAM for downstream processing. Preserve the reference build, index settings, read preprocessing, complete command, and Bowtie 2 version used in the analysis.
Research tasks
- Align relatively short DNA reads to a reference sequence
- Run local or end-to-end gapped alignment
- Process paired-end reads and produce SAM output
What to evaluate before use
- Bowtie 2 is optimized for relatively short reads against long references. It is not a drop-in replacement for Bowtie 1 and should not be assumed to suit every long-read task.
- Positions and mapping qualities remain uncertain in repetitive regions. A high overall alignment rate does not validate the sample, reference, or scientific conclusion.
Verification note
This entry summarizes the tool's role without assessing scientific accuracy or endorsing its outputs. Features and terms can change; consult the official source before adopting it for consequential work.
short-read alignmentreference genome
Last verified: 2026-09-07
Source: official documentation ↗