fasta-sanitize-pl

name	fasta-sanitize-pl
description	Use when sanitizing FASTA or FASTQ record names so they conform to SAM-compatible reference / read-name character rules.
disable-model-invocation	true
user-invocable	true

fasta-sanitize-pl

Quick Start

• Command: zcat input.fa.gz | /home/vimalinx/miniforge3/envs/bio/bin/fasta-sanitize.pl > output.fa
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/fasta-sanitize.pl
• Reference: references/help.md

When To Use This Tool

• Rewrite invalid FASTA / FASTQ record names before alignment or downstream SAM / VCF generation.
• Keep reference names consistent with SAM naming constraints early in the workflow.
• Sanitize both FASTA and FASTQ headers with one streaming pass.

Common Patterns

# 1) Sanitize a FASTA stream before indexing or alignment
zcat input.fa.gz | \
  /home/vimalinx/miniforge3/envs/bio/bin/fasta-sanitize.pl \
  > clean.fa

# 2) Sanitize FASTQ headers in a streaming pipeline
zcat reads.fq.gz | \
  /home/vimalinx/miniforge3/envs/bio/bin/fasta-sanitize.pl \
  > clean.fq

Recommended Workflow

1. Run it before alignment or any step that depends on consistent SAM-compatible names.
2. Capture stdout to a new FASTA / FASTQ file.
3. Watch stderr for Renaming reference ... messages.
4. Rebuild any downstream indices from the sanitized file rather than mixing old names with new ones.

Guardrails

• The tool does not support --help or --version flags; it expects file arguments.
• It autodetects FASTQ by @ headers and handles quality blocks, not just FASTA.
• Only the first whitespace-delimited token in the header is sanitized as the record name; trailing descriptive text is preserved.
• Valid names pass through unchanged, so not every file will emit rename messages on stderr.