search

pilirod70 / ngopt

Automatically exported from code.google.com/p/ngopt
Other
0 stars 0 forks source link

insert size estimation bug #4

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
First off, thanks for creating the pipeline. My tests comparing de novo 
illumina paired end assemblies of methanogen genomes versus closed (or almost 
closed) versions of the genomes shows that your pipeline works better than 
Velvet, Newbler, CLC Genomics, and SPADES in terms of contiguity and fidelity 
(ie miscalled bases).

I've been using different numbers of reads for input and noticed a possible bug 
with the insert size estimation. When using 2 million read pairs, the insert 
size is estimated as 100bp. However, when using greater numbers of reads (4 
million - 10 million), the insert size is ~430bp, which is what it should be.

I've tried supplying an insert size in a library file, but since the insert 
size can be estimated (i.e. 100bp), my provided insert size is not used.

Thanks again for constructing the pipeline.

Nick

Original issue reported on code.google.com by nyoun...@gmail.com on 30 Oct 2012 at 3:49