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
===== Require Jellyfish to be installed.
=====
make
=====
Usage: ./dd_unitigs.sh <fasta> <k>
./dd_unitigs.sh example/ref.fa 31
Output: File named uni_dd.fa containing double directed unitigs.
./directed_unitigs.sh example/ref.fa 31
Output: File named uni_directed.fa containing basic directed unitigs.
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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,
}