bowtie2-align-s

name	bowtie2-align-s
description	Use when aligning sequencing reads (FASTQ/FASTA) to a reference genome using Bowtie 2. Supports paired-end, unpaired, interleaved, and BAM inputs with SAM output.
disable-model-invocation	true
user-invocable	true

bowtie2-align-s

Quick Start

• Command: bowtie2-align-s -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bowtie2-align-s
• Full options: See references/help.md

When To Use This Tool

• Use bowtie2-align-s when aligning reads against a standard Bowtie 2 small index (.bt2).
• It is appropriate for FASTQ, FASTA, raw-read, interleaved, or name-sorted unaligned BAM inputs.
• Use it when you explicitly want the small-index aligner instead of the generic bowtie2 wrapper.
• In most everyday pipelines, the wrapper bowtie2 remains the safer default unless you need to pin the underlying binary.

Common Patterns

# Align unpaired reads against a standard Bowtie 2 index
bowtie2-align-s -x ref -U reads.fq -S aln.sam

# Align paired-end reads and use 8 threads
bowtie2-align-s -x ref -1 reads_R1.fq -2 reads_R2.fq -p 8 -S aln.sam

# Use local alignment with a sensitive preset
bowtie2-align-s -x ref -U reads.fq --very-sensitive-local -S aln.sam

# Suppress unaligned reads in SAM output
bowtie2-align-s -x ref -U reads.fq --no-unal -S aln.sam

Recommended Workflow

1. Ensure a Bowtie 2 index exists at <bt2-idx> (built with bowtie2-build; Bowtie 1 indexes are incompatible)
2. Prepare reads in FASTQ (default), FASTA (-f), or other supported formats
3. Run alignment: bowtie2-align-s -x <bt2-idx> -U reads.fq -S output.sam (add -p N for multithreading)
4. Optionally use presets (e.g., --very-sensitive) or reporting options (-k, -a, --no-unal)

Guardrails

• The tool warns that running bowtie2-align directly is not recommended; prefer the bowtie2 wrapper for typical use
• MAPQ values are not meaningful when using -k or -a reporting modes
• Use -I/-X to set min/max fragment length for paired-end; defaults are 0 and 500