A binfie’s garret

I'm a researcher in microbial genomics and bioinformatics, loving the bridge between molecular biology and computer science. I am currently at the Quadram Institute in Norwich.

Some Articles

Bash tutorial (part 1)
For loops (Bash scripting, part 2)
If, then. Condition checking for Bash scripts (Bash scripting, part 3)
Bash scripting safety net (Bash scripting, part 4)

Recent Posts

Generating latin bacterial names with GAN

04 Dec 2020
paper

Mark J. Pallen, Andrea Telatin, Aharon Oren
The Next Million Names for Archaea and Bacteria

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The Nim programming language for bioinformatics

12 Aug 2020
coding

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.

I started my best journey in a programming language.

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Revamping the N50 utility with new metrics

21 Apr 2020
coding

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.

I tried to make its bundled utility, called simply n50, useful both for interactive sessions and for scripts, and the utility itself has been my first tool packaged in bioconda.

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And less recent posts

07 Mar 2020 Bioinformatics papers as they should work
28 Jan 2020 Nannochloropsis genome portal end of life
23 Jan 2020 Online POD preview
09 Jan 2020 covtobed, the lost software
19 Aug 2019 N50 with conda
20 Jul 2019 Continuous integration can be addictive

GitHub