How do I install the Blast Formatter skill?

Run npx skillmds add vimalinx/blast-formatter 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 Blast Formatter 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 Blast Formatter?

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 Blast Formatter free to use?

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

Who published Blast Formatter?

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

Blast Formatter by vimalinx — Agent Skill

Name: Blast Formatter
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

blast-formatter

Quick Start

Command: blast_formatter -archive <archive.asn> -outfmt <format> -out <output>
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blast_formatter
Version: 2.17.0+
Full reference: See references/help.md

When To Use This Tool

Reformat a saved BLAST archive (outfmt 11) into tabular, XML, JSON, SAM, pairwise text, or HTML output.
Render the same search result in multiple formats without recomputing the alignment search.
Pull results by RID after a remote BLAST job finishes.
Define custom tabular field lists once the archive already exists.

Common Patterns

# 1) Reformat a saved archive as tabular output
blast_formatter \
  -archive search.asn \
  -outfmt "6 qaccver saccver pident length evalue bitscore" \
  -out hits.tsv

# 2) Generate an HTML report from the same archive
blast_formatter \
  -archive search.asn \
  -html \
  -outfmt 0 \
  -out report.html

# 3) Retrieve and format a completed remote search by RID
blast_formatter \
  -rid RID_VALUE \
  -outfmt 5 \
  -out result.xml

Recommended Workflow

Save BLAST searches as archive format (-outfmt 11) whenever you may want multiple downstream renderings.
Reformat the archive into the specific machine-readable or human-readable representation you need.
Use custom field lists with -outfmt 6, 7, 10, 17, or 20 instead of accepting defaults blindly.
Keep the original archive so you can regenerate other views later.

Guardrails

-archive and -rid are mutually exclusive inputs.
This tool does not rerun BLAST; it only formats an archive or completed remote request.
-max_target_seqs cannot be combined with -num_descriptions or -num_alignments.
The command name on disk is blast_formatter even though this skill is named blast-formatter.

---name: blast-formatterdescription: Use when you need to reformat BLAST archive files into different output formats (tabular, HTML, custom) without re-running the BLAST search.--- # blast-formatter ## Quick Start - **Command:** `blast_formatter -archive <archive.asn> -outfmt <format> -out <output>` - **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/blast_formatter` - **Version:** 2.17.0+ - **Full reference:** See `references/help.md` ## When To Use This Tool - Reformat a saved BLAST archive (`outfmt 11`) into tabular, XML, JSON, SAM, pairwise text, or HTML output. - Render the same search result in multiple formats without recomputing the alignment search. - Pull results by RID after a remote BLAST job finishes. - Define custom tabular field lists once the archive already exists. ## Common Patterns ```bash # 1) Reformat a saved archive as tabular output blast_formatter \ -archive search.asn \ -outfmt "6 qaccver saccver pident length evalue bitscore" \ -out hits.tsv ``` ```bash # 2) Generate an HTML report from the same archive blast_formatter \ -archive search.asn \ -html \ -outfmt 0 \ -out report.html ``` ```bash # 3) Retrieve and format a completed remote search by RID blast_formatter \ -rid RID_VALUE \ -outfmt 5 \ -out result.xml ``` ## Recommended Workflow 1. Save BLAST searches as archive format (`-outfmt 11`) whenever you may want multiple downstream renderings. 2. Reformat the archive into the specific machine-readable or human-readable representation you need. 3. Use custom field lists with `-outfmt 6`, `7`, `10`, `17`, or `20` instead of accepting defaults blindly. 4. Keep the original archive so you can regenerate other views later. ## Guardrails - `-archive` and `-rid` are mutually exclusive inputs. - This tool does not rerun BLAST; it only formats an archive or completed remote request. - `-max_target_seqs` cannot be combined with `-num_descriptions` or `-num_alignments`. - The command name on disk is `blast_formatter` even though this skill is named `blast-formatter`.

Frequently asked questions