MASH and khmer abundance

The other day at PHE we were investigating use of MASH sketches to find closest isolates. If you don’t already know about MASH, it’s a MinHash algorithm implemented by Adam Phillippy’s group (@aphillippy). It is fast and pretty neat, but the resulting distance is directly related to the errors in the sequencing. On one hand,…

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…