[khmer] diginorm on merged reads

Torsten Seemann torsten.seemann at monash.edu
Mon Oct 7 17:00:42 PDT 2013

> Following up on my previous question - I ran a few different assemblies
> exploring the effect of using khmer digital normalization and FLASH to
> merge short reads. I compared the results of (1) running diginorm only, (2)
> running diginorm than attempting to merge still-paired reads with FLASH,
> and (3) first attempting to merge paired reads with FLASH followed by
> diginorm. In all cases, I used trimmed-and-filtered reads and performed
> assembly using velvet-oases with a kmer of 21. Below are some assembly
> statistics.

I can confirm a similar result with a massive 200M read mouse-ish RNA-Seq
data set.

Using FLASH to overlap first giving ~280 bp SE reads, then doing Diginorm
(k=??) then  using Oases (k=61)  gave the 'best' txome assembly compared to
feeding read pairs. (and Trinity did 'worse' on everything, no matter what
we did, and took 1 week for each run).

It will eventually get published.

*--Dr Torsten Seemann
--Scientific Director : Victorian Bioinformatics Consortium, Monash
University, AUSTRALIA*
*--Acting Head : Life Sciences Computation Centre, VLSCI, Parkville,
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