LANGMEAD LAB @ JHU

Congratulations to the lab’s first PhD graduate, Jacob Pritt! He received his doctoral hood in a ceremony at Shriver Hall on Tuesday, May 21, 2019. Best of luck to Jacob who started a position as Junior Bio-Computational Scientist at Mimetics, a company specializing in analysis of dynamic biological networks. Photo courtesy of Nae-Chyun Chen.

Congratulations to PhD student Charlotte Darby for winning the RECOMB-seq 2019 Best Paper award for her paper “Samovar: Single-sample mosaic SNV calling with linked reads.” The preprint is available at: https://www.biorxiv.org/content/10.1101/560532v1, and the full paper is in press at iScience. Many thanks to the organizers for this honor! Samovar is a new software tool for…

PI Langmead co-authored a review describing how Bioinformatics training, with the assistance of cloud computing and open data in particular, can enhance STEM research in limited-resource countries and Universities. It appeared in Nature Biotechnology today. The review was primarily the work of Serghei Mangul and Lana Martin at UCLA. A trend highlighted here is the…

Congratulations to student Charlotte Darby for posting the Samovar preprint! Samovar is a new software tool for detecting mosaic single-nucleotide variants (SNVs) in linked-read whole-genome shotgun sequencing data. It calls mosaic SNVs within a single sample with accuracy comparable to what previously required trios or matched tumor/normal pairs and outperform single-sample mosaic variant callers. The…

A pan-genomics study “Efficient Construction of a Complete Index for Pan-Genomics Read Alignment” that we worked on with many collaborators — University of Florida (Boucher Lab), CeBiB and Diego Portales University (Travis Gagie), and University of Eastern Piedmond (Giovanni Manzini) — was accepted at the RECOMB2019 conference in Washington DC. Congratulations to Taher Mun, who…

Student Daniel Baker posted a preprint describing Dashing (https://github.com/dnbaker/dashing), a fast and accurate software tool for estimating similarities of genomes or sequencing datasets. It uses the HyperLogLog sketch together with cardinality estimation methods that specialize in set unions and intersections. Dashing sketches genomes more rapidly than previous MinHash-based methods such as Mash or BinDash while…

Jonathan Ling, together with Langmead lab members Chris Wilks and Rone Charles and collaborator Seth Blackshaw, posted a preprint describing ASCOT (http://ascot.cs.jhu.edu). The preprint is available at: https://www.biorxiv.org/content/early/2018/12/20/501882. ASCOT a new resource — building on the Snaptron (http://snaptron.cs.jhu.edu) tool and resource — allowing researchers to visualize and query alternative splicing patterns in public RNA-Seq data….

There has been a lot of interest in methods for building and aligning to graph genomes.  Graph genomes differ from typical “linear” reference genomes because they additionally take genetic variation into account. But basic questions remain: Which variants should we include in the reference? Is including more variants always better? How close these promising new…

In collaboration with groups at University of Florida (Boucher Lab), CeBiB and Diego Portales University (Travis Gagie), and University of Eastern Piedmond (Giovanni Manzini), Taher Mun and Ben Langmead released two preprints describing recent work on indexing and querying highly repetitive sequence collections. Both of the preprints — named “Prefix-Free Parsing for Building Big BWTs”…

Our work on improving thread-scaling in Bowtie, Bowtie 2 and HISAT appeared in Bioinformatics: https://doi.org/10.1093/bioinformatics/bty648. While work on efficient genomics software has generally focused on speed on a fixed, small number of threads, general-purpose processors are now capable of running hundreds of threads of execution simultaneously in parallel. Intel’s Xeon Phi Knights Landing architecture for…