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 | \ fastenshuffle | fastenmetrics | 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 using the following command:

cargo install fasten

Detailed information on how this works can be found in the cargo handbook at .

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 fastenshuffle.

--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

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

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.| |fastenvalidate | Validates your reads (deprecated in favor of fasteninspect and fasten_repair| |fasten_inspect | adds information to read IDs such as seqlength | |fasten_repair | Repairs corrupted reads | |fastenquality_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,

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