Adventures with Nanopore

This is a guest post by Alex Jironkin (@biocomputerist) in the core bioinformatics group at Colindale. TL;DR: Try assembling your hybrid Illumina-MinION data with smaller number of kmers for better assemblies By now you probably heard about the new Nanopore technology, it is truly marvellous bit of engineering. The DNA strands are pulled through the…

Clinical bioinformatics for microbiology

A week or two ago I went to an interesting meeting about the clinical bioinformatics training scheme. This is a clinical scientist training programme, akin to those that train clinical geneticists and microbiologists. The first cohort of 13 students are currently making their way through the scheme. I had a look through the curriculum after the…

What the phage is going on!?

This is a blog post by Lauren Cowley ——————————————————————————— TL;DR? A confusing difference in trimmed/non-trimmed velvet phage assemblies raised suspicions that it was a mixed phage culture Spades assembly seemed to show more than one phage present in the culture I concluded that spades is better than velvet at showing a representation of the whole…

Validation of BWA-mem

I have a new job! A couple of weeks ago I became a permanent employee of PHE. This new role will mean a shift from VTEC O157 to Salmonella. We have sequenced 1500 strains of Salmonella from diverse serotypes to validate serotyping via MLST (see Achtman et al., 2013 for more details). This is prior…