de novo assembly (SSAKE/VELVET)--- reverse complementary strand

[jtjli]

I'm running some denovo sequencing tools (SSAKE & Velvet) to build contigs from illumina data.

But somehow the tools don't seem to test & match the reverse complements of the sequences -- it seems like they assume all sequences are from the same strand. is this true??

Thanks
Jason

[francesco.vezzi]

I'm not sure about what SSAKE does, but VELVET test the overlaps also for reverse complementary. Instead of use SSAKE that is quite old i suggest you to try EDENA and EULER-SR that with VELVET are the best short read assemblers available in this moment