#bioinformatics #fastq #streaming

bin+lib fasten

A set of scripts to run basic analysis on fastq files

4 releases

Uses old Rust 2015

0.3.3 Aug 27, 2021
0.1.13 May 10, 2018
0.1.12 Apr 30, 2018
0.1.11 Apr 20, 2018
0.1.8 Apr 20, 2018

#104 in Science

MIT license

125KB
2K SLoC

Build Status Crates.io

Fasten

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

Synopsis

read metrics

$ cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | fasten_metrics | column -t
totalLength  numReads  avgReadLength  avgQual
800          8         100            19.53875

read cleaning

$ cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | \
    fasten_clean --paired-end --min-length 2 | \
    gzip -c > cleaned.shuffled.fastq.gz

$ zcat cleaned.shuffled.fastq.gz | fasten_metrics | column -t
totalLength  numReads  avgReadLength  avgQual
800          8         100            19.53875
# No reads were actually filtered with cleaning, with --min-length=2

etc

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
export PATH=$PATH:$(pwd)/fasten/target/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. (not currently implemented)
  • --paired-end Input reads are interleaved paired end
  • --verbose Print more status messages

Other documentation

  • Some workflows are shown in the one-liners page.
  • Some wrapper scripts are noted in the scripts page.

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_mutate introduce random mutations
fasten_regex Filter for reads using regex
fasten_progress Add progress to any place in the pipeline

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.

Dependencies

~9MB
~190K SLoC