Question: Using ABySS Tools for Ad Hoc OLC Assembly
gravatar for dbrowne.up
4.1 years ago by
United States
dbrowne.up70 wrote:


I have a set of contigs that I would like to re-assemble using an Overlap-Layout-Consensus (OLC)-type approach. Let's say the minimum contig size in the set is 1000 bp. If I understand correctly, the following commands should: 1) find all overlaps between 100-999 bp, and store that overlap information in the file; 2) clean up the overlap graph, ignoring contigs in the file REPEATS.fa, writing the assembled unambiguous paths to the file INPUT-1.path and the new graph to; then 3) merge unambiguously overlapping contigs using the information computed in the first two steps and write the merged sequences to INPUT-2.fa.

AdjList -v -k1000 -m100 INPUT-1.fa >
abyss-filtergraph -v -k1000 --dot --no-SS --assemble -g -i REPEATS.fa INPUT-1.fa >INPUT-1.path
MergeContigs -v -k1000 -o INPUT-2.fa --merged INPUT-1.fa INPUT-1.path

I know this is probably quite a crude approach, but would it achieve what I am trying to do? Any thoughts or suggestions otherwise are appreciated. I am happy to clarify any points that are unclear, if needed.




abyss assembly • 1.2k views
ADD COMMENTlink modified 4.1 years ago by benv710 • written 4.1 years ago by dbrowne.up70
gravatar for benv
4.1 years ago by
benv710 wrote:

Looks sensible to me.  I didn't realize that `abyss-filtergraph` could be used for the layout stage of assembly -- that is kind of neat.

As an alternative to `AdjList`, you may wish to try `abyss-overlap`.  And as an alternative to `abyss-filtergraph` you may wish to try `abyss-layout`.  I'm not really sure what the trade-offs are between those pairs of programs -- just giving you a heads up that those options are available too.

ADD COMMENTlink written 4.1 years ago by benv710

Thanks Ben! Quick follow-up question: how are transitive edges and shims defined? Just wondering whether or not I should aim to filter those out of the overlap graph prior to layout and consensus.

ADD REPLYlink written 4.1 years ago by dbrowne.up70
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 844 users visited in the last hour