#bioinformatics #fastq #friends

bin+lib ross

A set of scripts to run basic analysis on fastq files

2 releases

Uses old Rust 2015

0.1.7 Apr 20, 2018
0.1.6 Apr 19, 2018

#394 in Science

MIT license

115KB
1.5K SLoC

Build Status

Random Operations on Sequences Suite - ROSS

Perform random operations on fastq files, using unix streaming.

Installation

ROSS.rs 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 ROSS.rs
cargo build --release

All executables will be in the directory ROSS.rs/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 friends_joey.

  • --help
  • --numcpus Not all scripts will take advantage of numcpus.
  • --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.

Ross script descriptions

script Description
friends_monica Trims and cleans a fastq file. She likes to clean. Monica
friends_carol Convert any fastq file to a standard four-line-per-entry format. Carol can help straighten you out. Carol
friends_rachel Prints basic read metrics. Rachel tells you how good you look. Rachel
friends_ung Determines paired-endedness. Ugly naked guy has gone through a lot of scrutiny. UNG
friends_phoebe Randomizes reads. Phoebe is like, totally random. Phoebe
friends_emma Combines identical reads. Did you know that Emma was played by twins, Cali and Noelle Sheldon? Just like Michelle Tanner from Full House! UNG
friends_chandler Kmer counting. No outside dependencies. Chandler's job is rarely discussed but he does... I want to say, something in accounting? Chandler
friends_ursula Downsamples reads. Ursula is a twin but played by the same actress! Ursula
friends_joey Shuffles or deshuffles paired end reads. Joey can socialize! Joey
friends_barry Joins overlapping paired ends together. They might not always like it, but Barry can be a connection between friends of friends. Barry
friends_gunther Validates your reads ... and you Gunther
friends_quality_filter Transforms nucleotides to "N" if the quality is low
friends_trimmer Blunt-end trims reads
friends_replace Find and replace using regex
friends_regex Filter for reads using regex

Dependencies

~4.5MB
~100K SLoC

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