Scaffolding with ScaRa

ScaRa is our scaffolding tool that uses come concepts from the HERA scaffolder paper (https://www.biorxiv.org/content/early/2018/06/13/345983). This repository contains both Python and C++ implementations.

Installation

1. Clone the repository, and include all submodules.

git clone --recursive https://github.com/kkrizanovic/ScaRa.git

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

After cloning, Python scripts are ready to go.

2. Building C++ version

mkdir build
cd build
cmake ..
make

Dependencies

Python scripts require PYthon2.7. C++ version requires CMake 3.5.

Running Python version

ScaRa is run using <bridger.py> script from the root folder of the repository. Running the script without arguments will print out a help message. The script should be run wtith the first parameter set to scaffold in the following way:

bridger.py scaffold <contigs FASTA> <reads FASTA> <reads-contigs overlaps PAF/SAM> <reads-reads overlaps PAF/SAM options
options:"
-o (--output) <file> : output file to which the report will be written

Running C++ version

C++ executable should be in the build folder. Running it without arguments will print out following help message.

How to run ScaRa :
ScaRa -f (--folder) <Input folder>
    or
ScaRa -r <Reads file> -c <Contigs file> -o <Reads to Contigs Overlaps file> -s <Reads to Reds Overlaps file>
    The program will perform one iteration of the algorithm
    and output contigs to the standard output!.
    <Input foder> must contain the following files:
    - reads.fastq - reads in FASTQ/FASTA format
    - readsToContigs.paf - overlaps between reads and contigs
    - readsToReads.paf - overlaps between reads
    - contigs.fasta - contigs in FASTA format
If Reads file, Contigs file or Overlaps are specified,
they will not be looked for in the Input folder!
Options:
-f (--folder)     specify input folder for ScaRa
-r (--reads)      specify reads file for ScaRa
-c (--contigs)    specify contigs file ScaRa
-o (--overlapsRC)   specify contig-read overlaps file for ScaRa
-s (--overlapsRR)   specify read self overlaps file for ScaRa
-m (--multithreading)   use multithreading
-v (--version)    print program version
-h (--help)       print this help message

OLD ScaRa

Old ScaRa README (containing only the Python version) can be found at OLD ScaRa