GCSplit

Data partitioning algorithm for reduction of complexity and improvement of metagenomic assemblies.

Installation

To clone the repository, type git clone https://github.com/mirand863/gcsplit.git

To install GCSplit and its dependencies, type cd gcsplit, bash install.sh and source ~/.bashrc

Running

To see the usage just type gcsplit

GCSplit v1.2

A software to partition paired FASTQ files

Usage: gcsplit [options] -o <output_dir> 

Basic options:
    -o/--output <output_dir>    Folder to store all the files generated during the assembly (required).
    -p/--partitions <int>       Number of partitions [default: 16]
    -w/--whole                  Use whole dataset to merge [default: off]
    --iontorrent                This flag is required for IonTorrent data.
    -h/--help                   Prints this usage message.
    -v/--version                Prints version info

Input data:
    -f/--forward <filename>     File with forward paired-end reads.
    -r/--reverse <filename>     File with reverse paired-end reads.
    -s/--single <filename>      File with unpaired reads.

Advanced options:
    -t/--threads <int>          Number of threads [default: 4]
    -k/--kmers <int>            Number of kmers to run the assembly [default: 3]
    -m/--memory <int>           Set memory limit for SPAdes in Gb [default: 250]
    --only-assembler            Runs SPAdes on assembly mode only

Please, report bugs to: miranda.fmm@gmail.com
Software homepage: <https://github.com/mirand863/gcsplit>

Citation

If you use GCSplit, please cite:

Miranda F., Batista C., Silva A., Morais J., Neto N., Ramos R. (2018) Improving Metagenomic Assemblies Through Data Partitioning: A GC Content Approach. In: Rojas I., Ortuño F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2018. Lecture Notes in Computer Science, vol 10813. Springer, Cham.

@inproceedings{miranda2018gcsplit,
  author="Miranda, F{\'a}bio and Batista, Cassio and Silva, Artur and Morais, Jefferson and Neto, Nelson and Ramos, Rommel",
  editor="Rojas, Ignacio and Ortu{\~{n}}o, Francisco",
  title="Improving Metagenomic Assemblies Through Data Partitioning: A GC Content Approach",
  booktitle="Bioinformatics and Biomedical Engineering",
  year="2018",
  publisher="Springer International Publishing",
  address="Cham",
  pages="415--425",
  doi={10.1007/978-3-319-78723-7_36},
  url={https://doi.org/10.1007/978-3-319-78723-7_36},
  isbn="978-3-319-78723-7"
}