Genome Informatics Section

News

Human genome assemblies with nanopore, an update

May 23, 2018

We recently participated in a collaborative effort to sequence, assemble, and analyze a human genome (GM12878) using the Oxford Nanopore MinION (Jain et al. 2018). Since then, we’ve also developed a trio-based strategy for assembling complete haplotypes from long-read data (Koren et al. 2018). Oxford Nanopore has continued to advance in the meantime, releasing several major base-calling updates. Other tools, such as Nanopolish, have also gotten faster and added new functionality, like methylation-aware polishing. So, we decided to re-analyze the dataset from the paper using the latest base calling and assembly tools. The new assembly increases the NG50 to over 10 Mbp and trio binning accurately reconstructs key MHC genes for both haplotypes.

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. Update 2018-02-22: this position has now been filled.

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
RefSeq database growth influences the accuracy of k-mer-based species identification
bioRxiv, April 19, 2018
Nasko DJ, Koren S, Phillippy AM, Treangen TJ