Fasten

Perform random operations on fastq files, using unix streaming. Secure your analysis with Fasten!

Installation

Fasten is programmed in the Rust programming language. More information about Rust, including installation and the executable cargo, can be found at rust-lang.org.

After downloading, use the Rust executable cargo like so:

cd fasten
cargo build --release

All executables will be in the directory fasten/target/release.

General usage

All scripts accept the parameters, read uncompressed fastq format from stdin, and print uncompressed fastq format to stdout. All paired end fastq files must be in interleaved format, and they are written in interleaved format, except when deshuffling with fasten_shuffle.

--help
--numcpus Not all scripts will take advantage of numcpus.
--paired-end Input reads are interleaved paired end
--verbose Print more status messages

Fasten script descriptions

script	Description
`fasten_clean`	Trims and cleans a fastq file.
`fasten_straighten`	Convert any fastq file to a standard four-line-per-entry format.
`fasten_metrics`	Prints basic read metrics.
`fasten_pe`	Determines paired-endedness based on read IDs.
`fasten_randomize`	Randomizes reads from input
`fasten_combine`	Combines identical reads and updates quality scores.
`fasten_kmer`	Kmer counting.
`fasten_sample`	Downsamples reads.
`fasten_shuffle`	Shuffles or deshuffles paired end reads.
`fasten_validate`	Validates your reads
`fasten_quality_filter`	Transforms nucleotides to "N" if the quality is low
`fasten_trim`	Blunt-end trims reads
`fasten_replace`	Find and replace using regex
`fasten_regex`	Filter for reads using regex

Etymology

Many of these scripts have inspiration from the fastx toolkit, and I wanted to make a fasty which was already the name of a bioinformatics program. Therefore I cycled through other letters of the alphabet and came across "N." So it is possible to pronounce this project like "Fast-N" or in a way that indicates that you are securing your analysis by "fasten"ing it (with a silent T).

Acknowledgements

Thank you Henk Den Bakker for many helpful discussions around Rust, helping me name this software, and many other things.