Illumina 150PE Rocks!

Posted on Posted in Illumina

I have long drooled over the Illumina 150bp read length…

Once, a long time ago, soon after they were originally released, I got a single 150PE dataset– and was very dissapointed with the quality. With standard adapter read trimming (to PHRED=15), I trimmed almost every read down to 100bp- huge bummer as I have high hopes that 150bp will be significantly better than 100PE for de novo assembly.  Well, a few weeks ago I decided to give 150PE another try. The Illumina chemistry has improved, and hardware has updated as well (tho we still ‘only’ have the HiSeq2000).

Well let me tell you, the new 150PE rocks!  It is just as good as the 100PE. You do get some quality drop-off at the 3′ end, but it is much better. Generally, with 100bp reads I have come to expect to trim 10-20% of the data, and get beautiful reads in the end. Same thing for the 150PE.  As the images show, the mean PHRED score is >20 for all but the last 5 bases– and after trimming (10% of the data), quality scores are awesome.

I still need to compare these 150PE assemblies to 100PE assemblies, but my intuition is that they should be better-

Also, really interested in trying out FLASH or COPE to merge overlapping paired-end reads. I probably have a good bit of that, and hopefully that, too, will improve contiguity.