Thread scaling in Bioinformatics

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…

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Published:July 18, 2018 View Post

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Bowtie 2 at 10K citations

The study describing the Bowtie 2 read alignment tool has been cited over 10,000 times since it first appeared in April 2012, according to Google Scholar. The Langmead Lab continues its hard work improving and maintaining this open source software. We thank our funders for making this possible, especially the Intel Parallel Computing Program and…

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Published:June 10, 2018 View Post

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Ben wins teaching awards

From Ben: I had the honor of attending this year’s schoolwide convocation yesterday, where I received the Professor Joel Dean Excellence in Teaching Award from the CS department, as well as the William H. Huggins Award Excellence in Teaching Award from the Whiting School of Engineering.  Many thanks to all my students — your excellence and passion…

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Published:May 8, 2018 View Post

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FORGe preprint

There has been much interest in methods for building and aligning to “graph genomes,” which take variants into account when aligning sequencing reads. But basic questions remain: Which variants should we include in the reference? Is including more variants always better? How close these promising new methods come to the ideal of aligning to a…

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Published:April 30, 2018 View Post

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Charlotte’s HEART course

Charlotte Darby, a joint PhD student in the Langmead and Schatz labs, was highlighted in a recent news release for her work designing and teaching a course on complexity theory. The course is taught as part of the Hopkins Engineering Applications & Research Tutorials (HEART) program. HEART courses are small and taught by advanced graduate…

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Published:April 6, 2018 View Post

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recount2 wins Peer Prize

The recount2 project won the third edition of the Bioinformatics Peer Prize. The winner was decided by a vote of registered researchers across the globe and the prize is $2,000. Congratulations to lead authors Leo Collado-Torres and Abhi Nellore!

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Published:March 10, 2018 View Post

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Cloud review at NRG

A review paper describing advances in cloud computing, as well as how it has been applied in genomics research, was published online today in Nature Reviews Genetics.  Cloud computing went from a big idea to one of the most profitable parts of the tech sector in the span of about a decade.  DNA sequencing technology…

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Published:January 30, 2018 View Post

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New preprint on thread scaling

We posted a preprint on our thread scaling work in Bowtie, Bowtie 2 and HISAT: https://doi.org/10.1101/205328. 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…

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Published:October 25, 2017 View Post

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Snaptron in Bioinformatics

PhD student Chris Wilks’s paper describing Snaptron, a search engine for mRNA splicing patterns, appeared in the journal Bioinformatics today.  Snaptron is a search engine for querying splicing patterns in large, pre-analyzed collections of human RNA sequencing (RNA-seq) samples. Snaptron lends valuable context and support to hypotheses related to splicing patterns in human. Snaptron’s query…

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Published:September 1, 2017 View Post

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Qtip in Genome Biology

A new paper describing a tandem simulation framework for predicting mapping quality was published in Genome Biology.  The paper describes the free, open source Qtip software. Mapping qualities are important quantities in the world of next-gen sequencing analysis. A mapping quality quantifies the read aligner’s confidence that the reported alignment for a sequencing read is the correct…

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Published:August 14, 2017 View Post

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