fxtools

A collection of fasta/fastq related tools that I've needed to write.

Installation

# from crates.io
cargo install fxtools

# from github
git clone https://github.com/noamteyssier/fxtools
cd fxtools
cargo install --path .

Commands

Unique

This is a command that will determine all unique sequences within a fastx file and split the records into either unique or duplicates. It will also count the number of unique/duplicate sequences/duplicate records and report those. By default all unique reads will be pushed to stdout unless piped to a file with the -o flag. Nulled reads will not be reported by default but can be written to a filepath with the -n flag.

fxtools unique -i <input_fastx> -o <optional_output_file_for_unique> -n <optional_output_file_for_null>