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…
Or, how I failed advanced file copying. TL:DR? Phylogenetic trees can be hard to interpret – use bootstraps to help! Low coverage in one strain or having an outlier can screw with your tree Including positions that have been ignored due to low quality in some of your strains can be useful (i.e. use RAxML and…
I thought it might be fun to knock up a quick IPython notebook with some information about the number of e-burst groups (eBGs) within some of the more common (in the UK) Salmonella serotypes. At the moment, it can only be statically rendered, via a github gist and the IPython notebook viewer. Might look further into hosting…
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…
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…
This is a ‘write it down before I forget’ post. I have shared it in case anyone else is overcome by a sense of existential dread at having to use Bionumerics. Minimum spanning trees are a nice way to present data when you want to express the relationship between different genotypes you have observed and…
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…
Tanglegrams are a very cool way of visualising the difference between two trees. There is an implementation in Dendroscope that allows them to be made very easily, IF you know how (it isn’t covered very well in the documentation). This is how. This is definitely one of those, ‘write it down before I forget’ blogs.…
As the final part of my assembly optimisation I was interested in the impact of Titus Brown’s Khmer/Diginorm approach on speed and quality. Ten samples (VTECs sequenced on GAII) were assembled with a variety of pipelines: SPAdes corrected fastqs, assembled with SPAdes Khmer-ed fastqs, SPAdes corrected, assembled with SPAdes SPAdes corrected fastqs, assembled with Velvet…
We have seen significant differences between assemblies of shiga toxigenic E. coli genomes where the DNA was extracted with different protocols. In those experiments, I used Velvet for assembly and I wanted to check whether the difference we were seeing between the different extraction methods was somehow a Velvet artefact. The recent GAGE-B paper showed…
Bits and Bugs 