I’ve been working on a head to head comparison of the de novo transcriptome assemblers Trinity v.2.2.0 versus the new kids on the block – Shannon and BinPacker. The tl;dr version of the post is that these new assemblers are very good, and should be considered for new assembly projects, with just a couple of […]
A new transcriptome assembler has been released. Shanon: http://biorxiv.org/content/early/2016/02/09/039230 and http://sreeramkannan.github.io/Shannon/. It looks quite interesting from an algorithm standpoint and claims to be better than the existing suite of assemblers.. Good deal, I\’m all ears! I\’ll hope to provide a full review (with the lab) in a bit, but I have a few immediate suggestion after kicking […]
August 8 – August 19th, 2016 Kellogg Biological Station, Michigan State University To Apply: Fill out the form here: http://goo.gl/forms/jWE6fx4WP0. Due date 3/1/17 Course Directors: Matt MacManes, Assistant Professor, University of New Hampshire (@macmanes or matthew dot macmanes at unh dot edu) Meg Staton, Assistant Professor, University of Tennessee, Knoxville (@hardwoodgenomic or mstaton1 at utk […]
I\’ve been working on a project where I need to identify orthogroups – We used to use OrthoMCL for this, but it\’s very slooow. When I read a few months ago about OrthoFinder (http://www.genomebiology.com/2015/16/1/157, https://github.com/davidemms/OrthoFinder) I was pretty stoked cause it was faster and just as accurate or more. I\’ve run into a few issue, […]
CEGMA has been, for my lab, a really great tool for understanding genome assembly completeness and quality, so – that it has had so many problems recently has been a big problem. Never quite sure what exacty the issue is, is revolved around geneid not properly working.. (https://gist.github.com/macmanes/9cb776429df90723e3a9) is an example.. Anyway, to solve this […]
I was an early user of Tophat, way back before there were many good tools for quantitating expression from NGS reads. I was just learning how to process these types of data (e.g., learning a scripting language), so I thought that many of the problems I encountered were a result of my inadequacy — and […]
Ok, just a quick post here to verbalize something that bothers me (and everybody else, I suspect).. The issue of poor documentation of software.. Even ‘well’ documented programs have huge issues.. For instance, I am working with edgeR a lot lately.. The documentation is pretty good (link), but there is a lot still left up […]