Question: Mate pair Illumina reads - recommended mapper of choice, adapter removal and PE contamination
gravatar for Biomonika (Noolean)
6.1 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:


What is your mapper of choice for mate pairs generated by Illumina? I have heard about Novoalign, but haven't checked any newer options yet. (I know that some people just reverse complement the reads to PE orientation and then use their favorite mappers.)


Have you noticed any biotinylated adapters in your data? 


The protocol that Illumina uses for creating of mate-pair libraries doesn't generate only long mate-pair reads with expected insert sizes, but also proportion of reads in PE orientation, which are in this case "contamination". Here is the nice picture with insert sizes that illustrates this - PE contamination is in red and MP reads are in green.

Here is the link to Illumina mate pair protocol

I will appreciate your comments and shared experiences.

Thank you.

ADD COMMENTlink modified 6.1 years ago by 141341254653464453.5k • written 6.1 years ago by Biomonika (Noolean)3.1k
gravatar for 14134125465346445
6.1 years ago by
United Kingdom
141341254653464453.5k wrote:

The software NxTrim was recently released here:

ADD COMMENTlink written 6.1 years ago by 141341254653464453.5k

This looks absolutely wonderful! I will give it a try immediately. Thank you.

ADD REPLYlink written 6.1 years ago by Biomonika (Noolean)3.1k
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