Guideline to bioinformatics tools

Quality Assessment and Trimming Trimmomatic http://www.usadellab.org/cms/index.php?page=trimmomatic Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bolger, A. M., Lohse, M., & Usadel, B. (2014). Bioinformatics, btu170. A flexible read trimming tool that will remove Illumina adapters, reads below a certain length and low quality ends of the read Seqtk https://github.com/lh3/seqtk Tool for processing sequences in the FASTA…

My time, your time, compute time

I have recently started using the high performance cluster at the Sanger Institute, and it comes with an interesting quandary. You have to be explicit in the amount of RAM you request when you submit your job (the PHE cluster wasn’t like this). Then, that amount of RAM is assigned to your job and wont…

Cool built-in python tips and tricks

Travis Oliphant, who is involved with the really useful conda project, recently tweeted about David Beazley’s talk at pycon in chicago. Here’s the link to the whole thing, which is definitely worth watching. There are a few great tips in there, all around the idea that you only have to use python built-ins to do cool…

Doctor of the Rings?

My wonderful soon-to-be-wife just had her PhD viva and we were struck by the similarity between PhDs and Frodo’s journey in the Lord of the Rings. Turns out this guy got there first, but I think our theory still brings something to the table. The main parallel is that there are, like, a million endings!!!…

MASH and khmer abundance

The other day at PHE we were investigating use of MASH sketches to find closest isolates. If you don’t already know about MASH, it’s a MinHash algorithm implemented by Adam Phillippy’s group (@aphillippy). It is fast and pretty neat, but the resulting distance is directly related to the errors in the sequencing. On one hand,…

Plotting trees with plotTree

Kat Holt’s lab have a nice set of scripts that wrap around ete2 which makes it nice ‘n’ easy to annotate trees – plotTree! It works out the box! They have some great installation and usage instructions on the github, and some examples for the R half of the code, but the examples for the python bit are…