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.
friends_carol	Convert any fastq file to a standard four-line-per-entry format. Carol can help straighten you out.
friends_rachel	Prints basic read metrics. Rachel tells you how good you look.
friends_ung	Determines paired-endedness. Ugly naked guy has gone through a lot of scrutiny.
friends_phoebe	Randomizes reads. Phoebe is like, totally random.
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!
friends_chandler	Kmer counting. No outside dependencies. Chandler's job is rarely discussed but he does... I want to say, something in accounting?
friends_ursula	Downsamples reads. Ursula is a twin but played by the same actress!
friends_joey	Shuffles or deshuffles paired end reads. Joey can socialize!
friends_barry	Joins overlapping paired ends together. They might not always like it, but Barry can be a connection between friends of friends.
friends_gunther	Validates your reads ... and you
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