Duplication between the contig edges

[whchung]

Dear,

The latest version (1.3.2) of ABySS appealed to me to show good result
for one of my microbial genome project.

While in depth analysis of the contigs I found the ends of the contigs
were duplicated each other; from hundreds to thousands.

I think it is caused by that each contig is extended too much.

I have no idea to how reduce such duplication.

Any explanation or suggestion will be very helpful to my job.

Best,

Won-Hyong Chung
Korean Bioinformation Center, South Korea

[Shaun Jackman]

Hi Won-Hyong,

With a microbial assembly, ABySS will output lots of duplicated
overlapping sequence. You have a couple options. The first is to not use
the paired-end assembly. The file ${name}-3.fa should have much less
duplication, as overlapping contigs will overlap by exactly k-1 bp.
Next, you can increase the parameter s, which will result in smaller
contigs but less duplication. Finally, the file ${name}-contigs.dot
indicates which contigs overlap and by how much.

Sorry for the delay in my reply. Google Groups stopped sending me email
notifications of messages waiting for moderation.

Cheers,
Shaun