Question: Assembling PE reads with broad fragment length distribution
gravatar for bailliecharles
10 months ago by
bailliecharles0 wrote:


I am sequencing some very degraded DNA with 2X75bp PE. I have retained very short fragments ~40bp since these are useful for my application, did not perform fragmentation of my libraries due their being very degraded, and no size selection. What is the best way to do assembly since I cannot really say what the mean insert size is - most reads will overlap, and few will have inserts ~400 - 500bp.

Thanks, C

assembly • 221 views
ADD COMMENTlink modified 10 weeks ago by colindaven0 • written 10 months ago by bailliecharles0
gravatar for colindaven
10 weeks ago by
colindaven0 wrote:

Sounds tough. I like soapdenovo2 (install via bioconda), since it is easy to configure and runs quickly.

Another good assembler is Abyss.

I think you'll have to try a lot of assemblies to get something usable since the sample sounds poor.

ADD COMMENTlink written 10 weeks ago by colindaven0
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