Random Operations on Sequences Suite - ROSS
Perform random operations on fastq files, using unix streaming.
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
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
--numcpusNot all scripts will take advantage of numcpus.
--paired-endInput reads are interleaved paired end
--verbosePrint more status messages
- Some workflows are shown in the one-liners page.
- Some wrapper scripts are noted in the scripts page.
Ross script descriptions
||Trims and cleans a fastq file. She likes to clean.|
||Convert any fastq file to a standard four-line-per-entry format. Carol can help straighten you out.|
||Prints basic read metrics. Rachel tells you how good you look.|
||Determines paired-endedness. Ugly naked guy has gone through a lot of scrutiny.|
||Randomizes reads. Phoebe is like, totally random.|
||Combines identical reads. Did you know that Emma was played by twins, Cali and Noelle Sheldon? Just like Michelle Tanner from Full House!|
||Kmer counting. No outside dependencies. Chandler's job is rarely discussed but he does... I want to say, something in accounting?|
||Downsamples reads. Ursula is a twin but played by the same actress!|
||Shuffles or deshuffles paired end reads. Joey can socialize!|
||Joins overlapping paired ends together. They might not always like it, but Barry can be a connection between friends of friends.|
||Validates your reads ... and you|
||Transforms nucleotides to "N" if the quality is low|
||Blunt-end trims reads|
||Find and replace using regex|
||Filter for reads using regex|