reindex_assembly

This script changes the header of assembly FASTA (.fna) files.

Usage

reindex_assembly \
  --file /path/to/input.file \
  --out /path/to/output.file \
  --prefix STRAIN_scf \
  --leading_zeroes 5

Parameters

• --file: Path to the input FASTA file
• --out: Path to the output FASTA file
• --prefix: Prefix for the new sequence names (required)
• --leading_zeroes: Number of leading zeros in sequence names (optional, default: 5)

Example

This would transform a FASTA header like this >anything here into >STRAIN_scf_00001.

Help

reindex_assembly --help