LightStringGraph

Lightweight String Graph Construction

This software is in its initial stage of development. Please contact Marco Previtali for any questions or use the issue tracker for reporting bugs.

The software is composed of two different tools: lsg (light (string) overlap graph) and redbuild (string graph build).

To build both lsg and redbuild simply move in the root directory of the project and run make lsg redbuild.

If you want to try out the software on some (simulated or real) reads follow this steps:

1. download and compile BEETL (version 0.9.0 fixed to correctly compute LCP)
2. given a FASTA file a.fa (all the reads must have the same length), build the BWT with beetl bwt -i a.fa -o <BWTPrefix> -f ascii
3. run LightStringGraph ./bin/lsg -B <BWTPrefix> -T <Tau> -C <CycNum> where <Tau> is the minimum overlap between reads and <CycNum> >= <reads length> - <Tau>.
4. run redbuild ./bin/redbuild -b <BWTPrefix> -r a.fa -m <CycNum>+1 -l <ReadLength> and redirect STDOUT (the string graph in the ASQG format) to a file (you can compress it on the fly).