New publication: fast human read decontamination for SARS-CoV-2 Philip Fowler, 16th May 202216th May 2022 ReadItAndKeep is a new human-read decontamination algorithm that works by mapping the reads in a FASTQ file to the reference SARS-CoV-2 genome. This works because SARS-CoV-2 genetic variation is not so high as to lead to reads being incorrectly discarded and means the algorithm, which relies on minimap2, is both fast and has a low memory footprint. Published in Bioinformatics last week Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Related clinical microbiology computing gpas
New publication: detecting minor populations important for predicting fluoroquinolone resistance 5th April 20238th December 2023 When predicting if an infection is resistant or susceptible to a specific antibiotic, it is… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
antimicrobial resistance GARC: A Grammar for Antimicrobial Resistance Catalogues 25th November 201817th November 2020 During the CRyPTIC project it has become obvious that we need a grammar to describe… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
computing Running my first Software Carpentry workshop 1st November 2012 “Can you email me that script you used to do your analysis?” “Sure. It isn’t… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More