ross 0.1.7

A set of scripts to run basic analysis on fastq files
Documentation
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# 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](https://www.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](./docs/file-formats.md), 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](./docs/one-liners.md) page.
* Some wrapper scripts are noted in the [scripts](./docs/scripts.md) page.

## Ross script descriptions

|script               |Description|    |
|---------------------|-----------|----|
|`friends_monica`  | Trims and cleans a fastq file. She likes to clean.| ![Monica](/images/monica.jpg) |
|`friends_carol`   | Convert any fastq file to a standard four-line-per-entry format. Carol can help straighten you out.| ![Carol](/images/carol.jpg) | 
|`friends_rachel`  | Prints basic read metrics. Rachel tells you how good you look.| ![Rachel](/images/rachel.jpg) |
|`friends_ung`     | Determines paired-endedness. Ugly naked guy has gone through a lot of scrutiny.| ![UNG](/images/UNG.png) |
|`friends_phoebe`  | Randomizes reads. Phoebe is like, totally random.| ![Phoebe](/images/phoebe.png) |
|`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](/images/emma.png) |
|`friends_chandler`| Kmer counting. No outside dependencies. Chandler's job is rarely discussed but he does... I want to say, something in accounting?| ![Chandler](/images/chander.png) |
|`friends_ursula`  | Downsamples reads. Ursula is a twin but played by the same actress!| ![Ursula](/images/ursula.png) | 
|`friends_joey`    | Shuffles or deshuffles paired end reads. Joey can socialize!| ![Joey](/images/joey.png) |
|`friends_barry`   | Joins overlapping paired ends together. They might not always like it, but Barry can be a connection between friends of friends. | ![Barry](/images/barry.png) |
|`friends_gunther` | Validates your reads ... and *you* | ![Gunther](/images/gunther.png) |
|`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 | |