Standalone module for sampling genomic sequences. It supports two modes, random subsampling of sequencer data to a desired depth (given the reference length) and file splitting to desired size in bytes.

Rampler takes as first input argument a file in FASTA/FASTQ format which can be compressed with gzip. The rest of input parameters depend on the mode of operation. The output is stored into a file(s) which is in the same format as the input file but uncompressed.

1. gcc 4.8+ or clang 3.4+
2. cmake 3.2+

To install Rampler run the following commands:

git clone --recursive https://github.com/rvaser/rampler.git rampler
cd rampler
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make

After successful installation, an executable named rampler will appear in build/bin.

Optionally, you can run sudo make install to install rampler executable to your machine.

Note: if you omitted --recursive from git clone, run git submodule update --init --recursive before proceeding with compilation.

Usage of rampler is as following:

usage: rampler [options ...] <mode>

<mode>
    subsample <sequences> <reference length> <coverage> [<coverage> ...]

        <sequences>
            input file in FASTA/FASTQ format (can be compressed with gzip)
            containing sequences to be subsampled
        <reference length>
            integer denoting length of the reference genome (or
            assembly) from which the sequences originate
        <coverage>
            integer denoting desired coverage of the subsampled
            sequences

    split <sequences> <chunk size>

        <sequences>
            input file in FASTA/FASTQ format (can be compressed with gzip)
            containing sequences which will be split into smaller chunks
        <chunk size>
            integer denoting the desired chunk size in bytes

options:
    -o, --out-directory
        default: current directory
        path in which sampled files will be created
    --version
        prints the version number
    -h, --help
        prints out the help

For additional information, help and bug reports please send an email to one of the following: [email protected]

This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353.