Lightweight String Graph Construction
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 three different tools: lsg
(light (string) overlap graph), redbuild
(string graph build), and graph2asqg
(native graph format to ASQG).
To build all the tools simply move in the root directory of the project and run make all
.
If you want to try out the software on some (simulated or real) reads follow these steps:
a.fa
containing n
reads produce another FASTA file b.fa
containing 2n
reads s.t. reads between position 1
and n
are the same as those in a.fa
and reads between position n+1
and 2n
are their reverse and complement (for 1 <= i <= n
, read in position n+i
should be the reverse complement of read in position i
)cd <LSGPATH> && make all
b.fa
with beetl-bwt -i b.fa -o <BWTPrefix> --output-format=ASCII --generate-lcp --generate-end-pos-file
<LSGPATH>/bin/lsg -B <BWTPrefix> -T <Tau> -C <CycNum>
where <Tau>
is the minimum overlap between reads and <CycNum> >= <reads length> - <Tau>
<LSGPATH>/bin/redbuild -b <BWTPrefix> -r b.fa -m <CycNum>+1
<LSGPATH>/bin/graph2asqg -b <BWTPrefix> -r b.fa -l <readsLength>
and redirect STDOUT (the string graph in the ASQG format) to a file (you can compress it on the fly).If lsg
crashes and produces a logic error try to raise the limit on the maximum number of open file descriptors for the user running that command (for example, with the bash
built-in ulimit -n
) and delete all the *.tmplsg.*
files before running lsg
again.