BEDTools: The Swiss‐Army Tool for Genome Feature Analysis von Quinlan, Aaron R.

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Mosdepth: quick coverage calculation for genomes and exomes von Pedersen, Brent S, Quinlan, Aaron R

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BEDTools: a flexible suite of utilities for comparing genomic features von Quinlan, Aaron R., Hall, Ira M.

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Poretools: a toolkit for analyzing nanopore sequence data von Loman, Nicholas J, Quinlan, Aaron R

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GEMINI: integrative exploration of genetic variation and genome annotations von Paila, Umadevi, Chapman, Brad A, Kirchner, Rory, Quinlan, Aaron R

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LUMPY: a probabilistic framework for structural variant discovery von Layer, Ryan M, Chiang, Colby, Quinlan, Aaron R, Hall, Ira M

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A map of constrained coding regions in the human genome von Havrilla, James M., Pedersen, Brent S., Layer, Ryan M., Quinlan, Aaron R.

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Pybedtools: a flexible Python library for manipulating genomic datasets and annotations von Dale, Ryan K., Pedersen, Brent S., Quinlan, Aaron R.

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SpeedSeq: ultra-fast personal genome analysis and interpretation von 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

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GIGGLE: a search engine for large-scale integrated genome analysis von Layer, Ryan M, Pedersen, Brent S, DiSera, Tonya, Marth, Gabor T, Gertz, Jason, Quinlan, Aaron R

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Copy number variation detection and genotyping from exome sequence data von 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

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BamTools: a C++ API and toolkit for analyzing and managing BAM files von BARNETT, Derek W, GARRISON, Erik K, QUINLAN, Aaron R, STRÖMBERG, Michael P, MARTH, Gabor T

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Samplot: a platform for structural variant visual validation and automated filtering von Belyeu, Jonathan R., Chowdhury, Murad, Brown, Joseph, Pedersen, Brent S., Cormier, Michael J., Quinlan, Aaron R., Layer, Ryan M.

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Whole-genome sequencing analysis in families with recurrent pregnancy loss: A pilot study von 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

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Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation von Sasani, Thomas A, Pedersen, Brent S, Gao, Ziyue, Baird, Lisa, Przeworski, Molly, Jorde, Lynn B, Quinlan, Aaron R

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Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate von Nicholas, Thomas J, Cormier, Michael J, Quinlan, Aaron R

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Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls von Pedersen, Brent S, Quinlan, Aaron R

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Characterizing complex structural variation in germline and somatic genomes von Quinlan, Aaron R, Hall, Ira M

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Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies von Cormier, Michael J, Pedersen, Brent S, Bayrak-Toydemir, Pinar, Quinlan, Aaron R

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Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice von Sasani, Thomas A, Quinlan, Aaron R, Harris, Kelley

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