bowtie2sam-pl

name	bowtie2sam-pl
description	Use when converting legacy Bowtie text output into SAM and retaining only the best alignment per read.
disable-model-invocation	true
user-invocable	true

bowtie2sam-pl

Quick Start

• Command: bowtie2sam.pl alignments.bowtie > alignments.sam
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bowtie2sam.pl
• Reference: See references/help.md

When To Use This Tool

• Convert legacy tab-delimited Bowtie output into SAM.
• Collapse multiple Bowtie hits for a read down to a single best-hit SAM record.
• Preserve Bowtie-provided read sequence and quality strings while moving into SAM-compatible tooling.
• Use this only for old Bowtie text output, not for Bowtie's native SAM mode.

Common Patterns

# 1) Convert a Bowtie output file into SAM
bowtie2sam.pl \
  alignments.bowtie > alignments.sam

# 2) Stream Bowtie output directly into the converter
bowtie index reads.fq | bowtie2sam.pl > alignments.sam

# 3) Group by read name first if the Bowtie output was reordered
sort -k1,1 alignments.bowtie | bowtie2sam.pl > alignments.best.sam

Recommended Workflow

1. Confirm the input is legacy Bowtie text output rather than SAM emitted with Bowtie's own -S mode.
2. Keep alignments grouped by read name so the script can compare all hits for a read together.
3. Convert to SAM, then inspect a few records to confirm the chosen best hit and MAPQ behavior are sensible for your data.
4. If you need all multimapping hits, stop and use a different conversion route instead of this script.

Guardrails

• There is no real command-line help interface here: --help and --version are treated like filenames and can trigger file-open errors plus downstream warnings.
• The script emits one best alignment per read, not all reported Bowtie hits.
• Input should stay grouped by read name; otherwise best-hit selection can be wrong because the script resolves hits only within adjacent name blocks.
• Output is plain SAM records without a SAM header.