README.md

Modified-bcalm for directed unitigs

This tool computes directed and double directed unitigs from a FASTA/FASTQ file.

Note : This uses a modified version of bcalm in https://github.com/Malfoy/BCALM

Pre-requisites

===== Require Jellyfish to be installed.

Installation

===== make

Usage

=====

Usage: ./dd_unitigs.sh <fasta> <k>

To compute double directed unitigs:

./dd_unitigs.sh example/ref.fa 31
Output: File named uni_dd.fa containing double directed unitigs.

To compute basic directed unitigs:

./directed_unitigs.sh example/ref.fa 31
Output: File named uni_directed.fa containing basic directed unitigs.

License

=======

BCALM's license is BSD with Attribution. In informal words, any use is permitted as long as it acknowledges us. For example with a citation to:

@inproceedings{reprdbg14,
author = {Chikhi, R. and Limasset, A. and Jackman, S. and Simpson, J. and Medvedev, P.},
title = {{On the representation of de Bruijn graphs}},
booktitle = {RECOMB},
publisher = {Springer},
year = 2014,
}