Fasten

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_head	Get the first X reads or nts.
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 and/or removes adapter sequences
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

Benchmarking

Executables are benchmarked under GitHub Actions. A CI artifact is generated, and a composite image is available in the compressed file.

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

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