I first heard of nim discovering mosdepth, a fantastic program to extract coverage information from alignments. I just thought it was a bizarre choice and never thought again about it…until also Heng Li blogged about fast programming languages for bioinformatics.
My first Perl Module has been an N50 calculator, that to me is sort of an Hello World considering I spent most of my PhD trying to improve one (lovely) assembly.
During my PhD (2012), I made the Nannochloropsis gaditana genome portal, and also secured the nannochloropsis.org domain for it.
The Plain Old Documentation is probably only old, and no longer plain (who would say to prefer POD to MarkDown, for example)?
This tiny post is to celebrate my first Bioconda release, the handy n50 utility, that as the name implies calculates N50 from either FASTA or FASTQ files. The main use I did of this script was to quickly feed the output in bash scripts like:
After praising the romantic structure of the Perl testers grid, last week I started using Travis CI:
Travis CI is a hosted continuous integration service used to build and test software projects hosted at GitHub.
When I was attending my high school lessons, learning some programming was not so common, yet a computer magazine shipped with a free version of Borland Delphi, free because outdated (was for Windows 3.1, and it was alread 1998).
There are handy command line PDF manipulation tools, and while in the past I used several times
pdftk (to cut and paste pages…), I noticed that its installation in macOS is not as easy as it is under Linux, so I gave a try to
qpdf, that worked perfectly.
This April I started using
Dist::Zilla aka Maximum overkill for CPAN Authors.
This February I’ll deliver a second edition of the Bash for Bioinformatics training, at the Quadram Institute.
This is only a test, trying this vim powered website that I can update from any shell basically. Nice to type like it’s 1995, but times have changed and we are currently easily backed by a GitHub repository with some benefits like versioning.