md5fa

name	md5fa
description	Use when hashing FASTA records and comparing ordered versus order-insensitive sequence digests instead of taking a single whole-file MD5.
disable-model-invocation	true
user-invocable	true

md5fa

md5fa is an HTSlib-based FASTA digester. It emits one MD5 per FASTA record plus two aggregate summaries, >ordered and >unordered, so it is materially different from md5sum on the raw file bytes.

Quick Start

• Command: md5fa <fasta>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/md5fa
• Live output shape: md5 fasta_path record_label

When To Use This Tool

• Hash FASTA content at the record level instead of hashing the literal file bytes.
• Compare two FASTA files while distinguishing "same records, different order" from "different sequence content".
• Generate stable per-sequence digests for reference or manifest workflows.

Common Patterns

# 1) Hash every FASTA record plus aggregate ordered/unordered summaries
md5fa sample.fa

# 2) Use the >unordered line when record order should not matter
md5fa a.fa
md5fa b.fa