Random Operations on Sequences Suite - ROSS

Perform random operations on reads files. Right now ROSS only supports fastq and fastq.gz format.

Deprecation

🛑 ROSS has been deprecated for some time now due to the newer repo ROSS. These executables are about 10-20x faster than ROSS and install very easily using cargo. https://github.com/lskatz/fasten

General usage

All scripts accept the parameters

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

Ross script descriptions

script	Description
friends_monica.pl	Trims and cleans a fastq file
friends_carol.pl	Convert any fastq file to a standard four-line-per-entry format
friends_rachel.pl	Prints basic read metrics
friends_ung.pl	Determines paired-endedness
friends_ross.pl	Makes sure a fastq file is in a standard format and is unbroken
friends_phoebe.pl	Randomizes reads
friends_chandler.pl	Pure perl kmer counting. No outside dependencies.
friends_marcel.pl	Rescores reads based on kmer abundance
friends_ursula.pl	Removes duplicate reads and/or downsamples reads
friends_joey.pl	Shuffles or deshuffles paired end reads
friends_barry.pl	Joins overlapping paired ends together
friends_charles.pl	Introduces Ns into a read set to help simulate increasing ambiguities
friends_roger.pl	Finds invalid characters in a fastq file and fixes them

see also

ROSS.rs, a Rust implementation of ROSS https://github.com/lskatz/ROSS.rs