seqdupes

Removes duplicates from FASTA files. Supports filtering based on sequence content or header information.

Installation

Source

Download the source code and run:

cargo install

Usage

Run seqdupes to process FASTA files. You can specify whether to filter by sequence or by header.

Filtering by Sequence (default)

seqdupes -f path/to/sequence.fastq -j path/to/output.json > no_dupes.fas

Filtering by Header

If you prefer to filter duplicates based on headers rather than sequences, use the --by-header flag.

seqdupes -f path/to/sequence.fastq -j path/to/output.json --by-header > no_dupes.fas

Arguments

The tool outputs a FASTA file with duplicates removed to stdout and a JSON file containing details of the duplicates to the specified path.