I find myself continually frustrated**. Reading transcriptome assembly paper after paper, all of them quality trimming mindlessly at a Phred score 20 or 30. Why do people do this??!?!?! I just don\’t understand, given there is nary a shred of evidence to suggest its benefit, and a substantial amount of evidence to suggest the contrary […]

Earlier in the day, I said this: I don’t think Galaxy/CLC is the solution for biologists with genomic data.. These tools simply allow for sloppy and uninformed analyses. — Matt MacManes (@PeroMHC) August 30, 2014 Now, this is something that I have struggled with for the last few years.. Increasingly, people have been trying to […]

In my continuing quest to conquer fastQ, fastA, sam & bam files, I have accumulated several useful ‘tools’. Many of them are included in other software packages (e.g. SAMtools), but for some tasks, especially file management and  conversion, no standard toolkit exists, and instead researchers script their own solution. For me, sed and awk, along […]

I am writing this blog post in support of a paper that I have just submitted to arXiv: Improving transcriptome assembly through error correction of high-throughput sequence reads. My goal is not to talk about the nuts and bolts of the paper so much as it is to ramble about its motivation and the writing process. […]