How do I install the Bowtie2sam Pl skill?

Run npx skillmds add vimalinx/bowtie2sam-pl in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Bowtie2sam Pl safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Bowtie2sam Pl?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Bowtie2sam Pl free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Bowtie2sam Pl?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bowtie2sam Pl by vimalinx — Agent Skill

Name: Bowtie2sam Pl
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

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

Confirm the input is legacy Bowtie text output rather than SAM emitted with Bowtie's own -S mode.
Keep alignments grouped by read name so the script can compare all hits for a read together.
Convert to SAM, then inspect a few records to confirm the chosen best hit and MAPQ behavior are sensible for your data.
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.

---name: bowtie2sam-pldescription: Use when converting legacy Bowtie text output into SAM and retaining only the best alignment per read.--- # 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](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 ```bash # 1) Convert a Bowtie output file into SAM bowtie2sam.pl \ alignments.bowtie > alignments.sam ``` ```bash # 2) Stream Bowtie output directly into the converter bowtie index reads.fq | bowtie2sam.pl > alignments.sam ``` ```bash # 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.

Frequently asked questions