Search Results - "QUINLAN, Aaron R"

BEDTools: The Swiss-Army Tool for Genome Feature Analysis by Quinlan, Aaron R

“…Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse…”
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Mosdepth: quick coverage calculation for genomes and exomes by Pedersen, Brent S, Quinlan, Aaron R

“…Abstract Summary Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at…”
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BEDTools: a flexible suite of utilities for comparing genomic features by Quinlan, Aaron R., Hall, Ira M.

“…Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps…”
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Poretools: a toolkit for analyzing nanopore sequence data by Loman, Nicholas J, Quinlan, Aaron R

“…Nanopore sequencing may be the next disruptive technology in genomics, owing to its ability to detect single DNA molecules without prior amplification, lack of…”
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LUMPY: a probabilistic framework for structural variant discovery by Layer, Ryan M, Chiang, Colby, Quinlan, Aaron R, Hall, Ira M

“…Comprehensive discovery of structural variation (SV) from whole genome sequencing data requires multiple detection signals including read-pair, split-read,…”
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GEMINI: integrative exploration of genetic variation and genome annotations by Paila, Umadevi, Chapman, Brad A, Kirchner, Rory, Quinlan, Aaron R

“…Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of…”
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A map of constrained coding regions in the human genome by Havrilla, James M., Pedersen, Brent S., Layer, Ryan M., Quinlan, Aaron R.

“…Deep catalogs of genetic variation from thousands of humans enable the detection of intraspecies constraint by identifying coding regions with a scarcity of…”
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Pybedtools: a flexible Python library for manipulating genomic datasets and annotations by Dale, Ryan K., Pedersen, Brent S., Quinlan, Aaron R.

“…pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python…”
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SpeedSeq: ultra-fast personal genome analysis and interpretation by Chiang, Colby, Layer, Ryan M, Faust, Gregory G, Lindberg, Michael R, Rose, David B, Garrison, Erik P, Marth, Gabor T, Quinlan, Aaron R, Hall, Ira M

“…SpeedSeq is an open-source software suite offering very fast, accurate and comprehensive analysis of single-nucleotide and structural variants from whole…”
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GIGGLE: a search engine for large-scale integrated genome analysis by Layer, Ryan M, Pedersen, Brent S, DiSera, Tonya, Marth, Gabor T, Gertz, Jason, Quinlan, Aaron R

“…GIGGLE is a genome interval search engine that enables extremely fast queries of genome features from thousands of genome annotation sets. GIGGLE is a genomics…”
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Copy number variation detection and genotyping from exome sequence data by Krumm, Niklas, Sudmant, Peter H, Ko, Arthur, O'Roak, Brian J, Malig, Maika, Coe, Bradley P, Quinlan, Aaron R, Nickerson, Deborah A, Eichler, Evan E

“…While exome sequencing is readily amenable to single-nucleotide variant discovery, the sparse and nonuniform nature of the exome capture reaction has hindered…”
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BamTools: a C++ API and toolkit for analyzing and managing BAM files by BARNETT, Derek W, GARRISON, Erik K, QUINLAN, Aaron R, STRÖMBERG, Michael P, MARTH, Gabor T

“…Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging,…”
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Samplot: a platform for structural variant visual validation and automated filtering by Belyeu, Jonathan R, Chowdhury, Murad, Brown, Joseph, Pedersen, Brent S, Cormier, Michael J, Quinlan, Aaron R, Layer, Ryan M

“…Visual validation is an important step to minimize false-positive predictions from structural variant (SV) detection. We present Samplot, a tool for creating…”
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Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation by Sasani, Thomas A, Pedersen, Brent S, Gao, Ziyue, Baird, Lisa, Przeworski, Molly, Jorde, Lynn B, Quinlan, Aaron R

“…The number of de novo mutations (DNMs) found in an offspring's genome increases with both paternal and maternal age. But does the rate of mutation accumulation…”
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Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate by Nicholas, Thomas J, Cormier, Michael J, Quinlan, Aaron R

“…Identification of deleterious genetic variants using DNA sequencing data relies on increasingly detailed filtering strategies to isolate the small subset of…”
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Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls by Pedersen, Brent S, Quinlan, Aaron R

“…Most structural variant (SV) detection methods use clusters of discordant read-pair and split-read alignments to identify variants yet do not integrate depth…”
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Characterizing complex structural variation in germline and somatic genomes by Quinlan, Aaron R, Hall, Ira M

“…Genome structural variation (SV) is a major source of genetic diversity in mammals and a hallmark of cancer. Although SV is typically defined by its canonical…”
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Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies by Cormier, Michael J, Pedersen, Brent S, Bayrak-Toydemir, Pinar, Quinlan, Aaron R

“…Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A…”
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Whole-genome sequencing analysis in families with recurrent pregnancy loss: A pilot study by Workalemahu, Tsegaselassie, Avery, Cecile, Lopez, Sarah, Blue, Nathan R, Wallace, Amelia, Quinlan, Aaron R, Coon, Hilary, Warner, Derek, Varner, Michael W, Branch, D Ware, Jorde, Lynn B, Silver, Robert M

“…One to two percent of couples suffer recurrent pregnancy loss and over 50% of the cases are unexplained. Whole genome sequencing (WGS) analysis has the…”
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Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice by Sasani, Thomas A, Quinlan, Aaron R, Harris, Kelley

“…Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair,…”
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