Lib.rs

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#fastq #bioinformatics #streaming #stdin #stdio

bin+lib fasten

A set of scripts to run basic analysis on fastq files

by Lee Katz and 3 contributors

9 unstable releases (4 breaking)

Uses old Rust 2015

0.8.3 Feb 22, 2024
0.8.1 Feb 12, 2024
0.7.2 Oct 28, 2023
0.4.4 Mar 17, 2022
0.1.12 Apr 30, 2018

#22 in Biology

Download history 6/week @ 2024-09-20 2/week @ 2024-09-27

119 downloads per month

MIT license

165KB
2.5K SLoC

Fasten

Crates.io CI DOI

A powerful manipulation suite for interleaved fastq files. Executables can read/write to stdin and stdout, and they are compatible with the interleaved fastq format. This makes it much easier to perform streaming operations using unix pipes.

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

Installation

Installation from source

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)/target/release

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

note: there are some Makefile methods to help including

  • make all to make the following
    • make release install fast executables
    • make debug install executables quickly (although the executables will not be optimized)
    • make fasten/doc compile lastest documents
  • make clean uninstall local binaries

Installation without git

You can also install Fasten straight from https://crates.io using the following command:

cargo install fasten

Detailed information on how this works can be found in the cargo handbook at https://doc.rust-lang.org/cargo/commands/cargo-install.html.

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

Documentation

Please see the inline documentation at https://lskatz.github.io/fasten/fasten

This documentation was built with cargo doc --no-deps

Other documentation

  • Some wrapper scripts are noted in the scripts page.

Contributing

Instructions for how to contribute can be found in CONTRIBUTING.md.

Fasten script descriptions

All executables read and write in the fastq format except fasten_convert.

executable Description
fasten_clean Trims and cleans a fastq file.
fasten_convert Converts between different sequence formats like fastq, sam, fasta.
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_normalize Normalize read depth by using kmer counting.
fasten_sample Downsamples reads.
fasten_shuffle Shuffles or deshuffles paired end reads.
fasten_validate Validates your reads (deprecated in favor of fasten_inspect and fasten_repair
fasten_inspect adds information to read IDs such as seqlength
fasten_repair Repairs corrupted 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
fasten_sort Sort fastq entries

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).

Citation

DOI

To cite, please refer to Katz et al., (2024). Fasten: a toolkit for streaming operations on fastq files. Journal of Open Source Software, 9(94), 6030, https://doi.org/10.21105/joss.06030

Dependencies

~11MB
~189K SLoC