[khmer] Dealing with paired-End Data

Alexis Groppi alexis.groppi at u-bordeaux2.fr
Mon Mar 25 07:29:19 PDT 2013


Hi Titus,

May be a very dumb question :
How to deal with paired-end data (Illumina reads of 75 nt) ?
For some sample, I have paired-end data : it means 2 .fastq file 
(SampleN_R1.fastq and SampleN_R2fastq).
What is the best strategy :
a/ Treat each file (R1 and R2) separatly (normalization, filtering, 
partition) but then how to deal with the resulting files .part files 
from each R1 and R2 for assembly ?

b/ - pooling together these R1 and R2 for each sample
- then perform normalization, filtering, partition and then assembly 
considering these data as single end ?
Try to rebuild the pairs in each partition before assembly  and then 
assembly as paired-end ?

c/strip-and-split-for-assembly ?

d/ Other ?

Thanks for your help

Alexis

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