bowtie2-align-l

name	bowtie2-align-l
description	Use when aligning sequencing reads to a reference using Bowtie 2's large-index alignment engine.
disable-model-invocation	true
user-invocable	true

bowtie2-align-l

Quick Start

• Command: bowtie2-align-l
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bowtie2-align-l
• Full reference: See references/help.md for complete options

When To Use This Tool

• Use bowtie2-align-l when your reference was indexed in Bowtie 2 large-index format (.bt2l), typically for very large references.
• It is appropriate for aligning single-end, paired-end, interleaved, or name-sorted unaligned BAM reads against that large index.
• Use it when you specifically need the large-index binary, not the generic bowtie2 wrapper.
• Most routine workflows should still prefer the bowtie2 wrapper unless you need to force the large-index executable directly.

Common Patterns

# Align unpaired reads against a large Bowtie 2 index
bowtie2-align-l -x ref_large -U reads.fq -S aln.sam

# Align paired-end reads with multiple threads
bowtie2-align-l -x ref_large -1 reads_R1.fq -2 reads_R2.fq -p 8 -S aln.sam

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

# Report up to 5 alignments per read
bowtie2-align-l -x ref_large -U reads.fq -k 5 -S aln.sam

Recommended Workflow

1. Prepare index: Ensure a Bowtie 2 large index (.bt2l files) exists for your reference genome
2. Specify input: Provide reads via -1/-2 (paired), -U (unpaired), --interleaved, or -b (BAM)
3. Configure alignment: Select mode (--end-to-end or --local) and optionally a preset (e.g., --sensitive-local)
4. Execute and output: Run with -x <index>, input files, and -S <output.sam> (defaults to stdout)

Guardrails

• Use Bowtie 2 indexes only (.bt2l); Bowtie 1 indexes are not compatible
• Prefer sensitivity presets over manual parameter tuning unless profiling requires it
• Consider the bowtie2 wrapper script instead of direct invocation as recommended by the tool warning
• MAPQ is not meaningful in -k or -a multi-hit reporting modes