bowtie2

name	bowtie2
description	Use when aligning short reads to a reference genome or indexed sequence database. Suitable for mapping FASTQ/FASTA reads in paired-end or single-end mode to produce SAM output.
disable-model-invocation	true
user-invocable	true

bowtie2

Quick Start

• Command: bowtie2 -x <bt2-idx> -1 <m1> -2 <m2> -S <sam> or bowtie2 -x <bt2-idx> -U <r> -S <sam>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bowtie2
• Version: 2.5.5
• Full reference: See references/help.md for complete options and flags

When To Use This Tool

• Align short reads to a Bowtie2 index.
• Use for DNA or transcriptome-like short-read mapping where Bowtie2 behavior is already established in the workflow.
• Prefer Bowtie2 presets over micromanaging seed parameters on the first pass.
• Pair with bowtie2-build when the reference index still needs to be created.

Common Patterns

# 1) Paired-end end-to-end alignment
bowtie2 \
  -x ref_index \
  -1 sample_R1.fastq.gz \
  -2 sample_R2.fastq.gz \
  -p 16 \
  -S sample.sam

# 2) More sensitive local alignment
bowtie2 \
  --very-sensitive-local \
  -x ref_index \
  -U sample.fastq.gz \
  -p 8 \
  -S sample.sam

# 3) Interleaved input
bowtie2 \
  -x ref_index \
  --interleaved sample.interleaved.fastq.gz \
  -S sample.sam

Recommended Workflow

1. Build the index once with bowtie2-build.
2. Choose single-end, paired-end, interleaved, or BAM input mode explicitly.
3. Start with preset sensitivity options and only tune lower-level parameters if needed.
4. Convert and sort downstream with samtools, then review alignment summaries from stderr.

Guardrails

• Bowtie 1 and Bowtie 2 indexes are not compatible.
• -k and especially -a change reporting semantics; MAPQ becomes less interpretable in multi-hit reporting modes.
• --local allows soft clipping; use it intentionally rather than by habit.
• SAM output defaults to stdout, so -S or shell redirection should be explicit.