Accuracy, speed and error tolerance of short DNA sequence aligners

Over the past few years at GenomeSpot, I've evaluated alignment software accuracy for DNA-seq, RNA-seq and small RNA-seq. After discussions with colleagues and followers, I thought it was time to develop aspects of this work to a point where it would be publishable in journals. Over the past year I've put together a paper that comprehensively evaluated accuracy of small RNA aligners. After three review and revision cycles I'm happy to say it has been accepted for publication in RNA. It will likely appear in the August issue.

Secondly, I've extended upon work from a previous post where I evaluated the accuracy of several DNA-seq mappers with error containing reads, and did further work like:
  • varying the read length from 50 nt to 480 nt
  • performing parallel analysis with Arabidopsis and human
  • using simulators to generate Illumina and Ion Torrent read sets
  • tested the speed (throughput) of aligners with Illumina reads
This work was just made public today on bioaRxiv. Have a read and tell me what you think! Here's the Link.

I'm very supportive of the bioaRxiv model that allow rapid dissemination of research findings and invites the general scientific community to scrutinise the work publicly.


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