We’ve done a quick analysis on the meningitis outbreak genome to try and answer whether there is anything obviously genetically unusual about the publicly available outbreak strain.

We aimed for three things:

• To see if the outbreak genome is on an unusually long branch, or otherwise different phylogenetically from its neighbours.
• Look for where mutation/recombination has occurred on the branch leading to the outbreak.
• Look for any effect of phase variable loci in the outbreak.

The final one of these didn’t work reliably without a close high-quality reference and/or more careful analysis time.

This blog post summarises some checks and comprobations done while developing Sparrowhawk after we discovered an unsettling surprise. The first two sections explain quickly what a genomic assembler is and the issue we found during the development (bad performance when assembling at large k values), and why it prompted us to study hash collisions as a potential cause for this. If you are here only for the hashes and the collisions, jump directly to the third section (ntHash and collisions).

Introduction

The intersection of biology and computer science has given rise to the rapidly evolving field of bioinformatics. For aspiring scientists in this field, the opportunity to work alongside leading experts at a research institute is a unique experience. Each year, the French Embassy Internship Program makes this dream a reality for a small group of French students, opening the doors to EMBL-EBI.