SPUMONI in iScience

A team led by Ph.D. student Omar Ahmed just published a journal paper in iScience describing a novel method and new software tool called SPUMONI.  SPUMONI can rapidly match sequencing reads to a pan-genome index, i.e. an index consisting of many strains or individuals.  At SPUMONI’s core is a novel algorithm for computing “matching statistics” against an…

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Published:June 14, 2021 View Post

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levioSAM in Bioinformatics

Students Taher Mun and Nae-Chyun Chen published an Application Note in the journal Bioinformatics describing a new tool called levioSAM. As more population genetics datasets and population-specific references become available, the task of translating (“lifting”) read alignments from one reference coordinate system to another is becoming more common. LevioSAM is a tool for lifting SAM/BAM…

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Published:June 5, 2021 View Post

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recount3 preprint

We posted a preprint today describing the new recount3 resource.  This effort was led by (now graduated) Ph.D. student Chris Wilks and spanned multiple research groups including our group, Kasper Hansen’s group and Leonardo Collado Torres’ group. recount3 is a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly…

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Published:May 24, 2021 View Post

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Minicore preprint

Ph.D. student Daniel Baker posted a preprint describing a new software library called Minicore for fast k-means clustering of single-cell RNA sequencing (scRNA-seq) data.  Minicore works with sparse count data — which is the form scRNA-seq data usually starts in —  as well as with dense data from after dimensionality reduction. Minicore uses a novel vectorized weighted…

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Published:May 24, 2021 View Post

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SPUMONI preprint

A team led by Ph.D. student Omar Ahmed posted a preprint describing a novel method and new software tool called SPUMONI.  SPUMONI can rapidly match sequencing reads to a pan-genome index, i.e. an index consisting of many strains or individuals.  At SPUMONI’s core is a novel algorithm for computing “matching statistics” against an efficient kind…

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Published:May 24, 2021 View Post

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Megadepth in Bioinformatics

A team led by (now graduated) Ph.D. student Chris Wilks published a new study in the journal Bioinformatics describing the software tool Megadepth.  Megadepth is a fast tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files — i.e. summing or averaging the depth of coverage over genomic intervals.  It uses substantially less…

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Published:May 24, 2021 View Post

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New funded R01 & R35 projects

The Langmead Lab is starting the new year with two new funded projects. One is an R01 from NIH/NHGRI funding our work on addressing reference bias with personal and panel references. This is joint work with Christina Boucher at University of Florida and Travis Gagie at Dalhousie University. Our recent paper on the Reference Flow…

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Published:January 4, 2021 View Post

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Reference flow in GB

Nae-Chyun’s paper describing the “reference flow” alignment framework appeared in the journal Genome Biology today. Most sequencing data analyses start by aligning sequencing reads to a linear reference genome, consisting of one string per chromosome. But a linear reference is an arbitrary point of reference; using a single linear reference causes “reference bias,” a tendency…

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Published:January 4, 2021 View Post

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Chris defends

Huge congratulations to Chris Wilks, who successfully completed his Ph.D. defense on September 30th! Chris’ thesis, titled “Enabling Efficient and Streamlined Access to Large Scale Genomic Expression and Splicing Data”covers his work on Snaptron (paper), the recount3 project, a recent project studying alignment errors in long-read RNA-seq datasets, and several other collaborative efforts (e.g. Rail-RNA,…

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Published:October 23, 2020 View Post

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Charlotte defends

Huge congratulations to Charlotte Darby, who successfully completed her Ph.D. defense on May 26th! Charlotte’s thesis, titled “Computational methods addressing genetic variation in next-generation sequencing data” covers her work on Samovar (paper), scHLAcount (paper) and Vargas (paper), among other projects. Charlotte was co-advised by Ben and by Dr. Mike Schatz. Next, Charlotte will join Rahul…

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Published:June 28, 2020 View Post

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