Genome Informatics Section


We are hiring!

October 4, 2017

The Genome Informatics Section is hiring! Come and join our outstanding team at the National Human Genome Research Institute. The official advertisement is for a postdoctoral position, but we will also consider outstanding postbacs or graduate students (via the NIH GPP). Simply follow the same application procedure described below.

Mash Screen: what's in my sequencing run?

September 25, 2017

Last year we published Mash (Ondov et al. 2016) for the rapid comparison of genomes and metagenomes. Mash builds on Andrei Broder’s foundational paper “On the resemblance and containment of documents” (Broder 1997), and uses the MinHash technique to rapidly estimate resemblance, e.g. the similarity of two whole genomes. Mash is great for this purpose, but is not well suited for estimating containment, e.g. detecting genomes contained within a metagenome. Implementing containment was the next logical step for Mash — it is in the title of the Broder paper, after all! Here we introduce a new Mash screen operation that implements containment in the context of genomics.



A single molecule sequence assembler for genomes large and small


Fast genome and metagenome distance and containment estimation using MinHash
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads
BMC Biology, January 11, 2018
Eccles D, Chandler J, Camberis M, Henrissat B, Koren S, Gros GL, Ewbank JJ
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation
Gigascience, January 10, 2018
Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen BD, Chen X, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, Sutton GG, Phillippy AM, Piermarini PM, Shabman RS