How do I install the Blast2sam Pl skill?

Run npx skillmds add vimalinx/blast2sam-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 Blast2sam Pl safe to use?

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Which AI agents work with Blast2sam 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 Blast2sam Pl free to use?

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

Who published Blast2sam Pl?

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

Blast2sam Pl by vimalinx — Agent Skill

Name: Blast2sam Pl
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

blast2sam-pl

Quick Start

Command: blast2sam.pl [-s] [-d] input.blast > output.sam
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blast2sam.pl
Full reference: See references/help.md

When To Use This Tool

Convert legacy default-format blastn text output into SAM records.
Bridge older BLAST workflows into samtools or other SAM/BAM-aware tooling.
Emit aligned query sequence with -s when downstream tools need SAM field 10 populated.
Emit dummy quality scores with -d when a downstream parser insists on SAM field 11.

Common Patterns

# 1) Convert legacy BLASTN text output into headerless SAM
blast2sam.pl \
  alignments.blast > alignments.sam

# 2) Include aligned query sequence plus dummy qualities
blast2sam.pl \
  -sd \
  alignments.blast > alignments.with-seq.sam

# 3) Add a SAM header afterwards for downstream tools that require one
blast2sam.pl -sd alignments.blast > alignments.sam
samtools view -hT reference.fa alignments.sam > alignments.with-header.sam

Recommended Workflow

Generate legacy blastn output in the default pairwise text format, not tabular or XML output.
Convert it with blast2sam.pl, adding -s if downstream tools need sequence and -d if they also need quality strings.
Add a SAM header separately if the next tool expects one.
Inspect a few records before batch conversion, especially strand flag, position, CIGAR, and sequence fields.

Guardrails

This parser is tailored to legacy plain-text blastn output; it is not the right tool for BLAST tabular, XML, JSON, or generic BLAST+ -outfmt outputs.
--help works via Perl Getopt::Std, but -help is wrong here and is split into -h -e -l -p, which produces unknown-option errors.
-s prints the aligned query sequence, not necessarily the original full read sequence from FASTQ input.
-d fills SAM field 11 with dummy I characters (Phred 40 style); use that only when fake quality scores are acceptable.
Output is headerless and queries without alignments are omitted rather than emitted as unmapped SAM records.

---name: blast2sam-pldescription: Use when converting legacy plain-text blastn output into SAM records for downstream SAM/BAM-compatible tooling.--- # blast2sam-pl ## Quick Start - **Command**: `blast2sam.pl [-s] [-d] input.blast > output.sam` - **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/blast2sam.pl` - **Full reference**: See [references/help.md](references/help.md) ## When To Use This Tool - Convert legacy default-format `blastn` text output into SAM records. - Bridge older BLAST workflows into `samtools` or other SAM/BAM-aware tooling. - Emit aligned query sequence with `-s` when downstream tools need SAM field 10 populated. - Emit dummy quality scores with `-d` when a downstream parser insists on SAM field 11. ## Common Patterns ```bash # 1) Convert legacy BLASTN text output into headerless SAM blast2sam.pl \ alignments.blast > alignments.sam ``` ```bash # 2) Include aligned query sequence plus dummy qualities blast2sam.pl \ -sd \ alignments.blast > alignments.with-seq.sam ``` ```bash # 3) Add a SAM header afterwards for downstream tools that require one blast2sam.pl -sd alignments.blast > alignments.sam samtools view -hT reference.fa alignments.sam > alignments.with-header.sam ``` ## Recommended Workflow 1. Generate legacy `blastn` output in the default pairwise text format, not tabular or XML output. 2. Convert it with `blast2sam.pl`, adding `-s` if downstream tools need sequence and `-d` if they also need quality strings. 3. Add a SAM header separately if the next tool expects one. 4. Inspect a few records before batch conversion, especially strand flag, position, CIGAR, and sequence fields. ## Guardrails - This parser is tailored to legacy plain-text `blastn` output; it is not the right tool for BLAST tabular, XML, JSON, or generic BLAST+ `-outfmt` outputs. - `--help` works via Perl `Getopt::Std`, but `-help` is wrong here and is split into `-h -e -l -p`, which produces unknown-option errors. - `-s` prints the aligned query sequence, not necessarily the original full read sequence from FASTQ input. - `-d` fills SAM field 11 with dummy `I` characters (Phred 40 style); use that only when fake quality scores are acceptable. - Output is headerless and queries without alignments are omitted rather than emitted as unmapped SAM records.

Frequently asked questions