Genome Informatics Section

News

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.

People
Software

Canu

A single molecule sequence assembler for genomes large and small

Mash

Fast genome and metagenome distance and containment estimation using MinHash
Publications
De novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
Plant Cell, October 13, 2017
Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat RT, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger A, Usadel B
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
Briefings in Bioinformatics, August 7, 2017
Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M