BEDOPS: high-performance genomic feature operations.

Bioinformatics
Shane NephJohn A Stamatoyannopoulos

Abstract

The large and growing number of genome-wide datasets highlights the need for high-performance feature analysis and data comparison methods, in addition to efficient data storage and retrieval techniques. We introduce BEDOPS, a software suite for common genomic analysis tasks which offers improved flexibility, scalability and execution time characteristics over previously published packages. The suite includes a utility to compress large inputs into a lossless format that can provide greater space savings and faster data extractions than alternatives. http://code.google.com/p/bedops/ includes binaries, source and documentation.

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Citations

Nov 7, 2012·Bioinformatics·Ryan M LayerAaron R Quinlan
Mar 19, 2013·Bioinformatics·Glenn HickeyDavid Haussler
Sep 8, 2012·Genome Research·Benjamin VernotJoshua M Akey
Sep 8, 2012·Genome Research·Hao WangJohn A Stamatoyannopoulos
Sep 8, 2012·Science·Matthew T MauranoJohn A Stamatoyannopoulos
Mar 8, 2014·PLoS Genetics·Darren A CusanovichYoav Gilad
May 9, 2014·PloS One·Hashem KoohyTim Hubbard
Jun 10, 2014·PloS One·Giovanni Marco Dall'OlioHafid Laayouni
Jan 31, 2014·Science·Benjamin Vernot, Joshua M Akey
Dec 18, 2013·Science·Andrew B StergachisJohn A Stamatoyannopoulos
Dec 18, 2013·Nature Biotechnology·Paz PolakShamil R Sunyaev
May 17, 2014·Cancer Chemotherapy and Pharmacology·Wendi V RodriguezaAyad Al-Katib
Nov 21, 2014·Nature·Andrew B StergachisJohn A Stamatoyannopoulos
Oct 6, 2014·Nature Structural & Molecular Biology·David R DeyleDavid W Russell
Aug 14, 2013·Journal of Biosciences·Michel Morange
Jan 7, 2015·Journal of Cellular Biochemistry·Matloob Khushi
Apr 15, 2015·Journal of Molecular and Cellular Cardiology·Mark P WhiteDeepak Srivastava
Dec 5, 2014·Genome Medicine·Graham Rs Ritchie, Paul Flicek
Oct 27, 2015·Nature Genetics·Matthew T MauranoJohn A Stamatoyannopoulos
Sep 24, 2015·Human Molecular Genetics·Sina A GharibUNKNOWN SpiroMeta Consortium
Oct 5, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Gordon GremmeStefan Kurtz
May 25, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Kristian OvaskaSampsa Hautaniemi
Mar 26, 2016·Briefings in Bioinformatics·Vahid JaliliMarco Masseroli
Mar 29, 2016·Nature Genetics·Walter L EckalbarNadav Ahituv
Aug 11, 2015·Cell Reports·Matthew T MauranoJohn A Stamatoyannopoulos
Feb 5, 2015·Bioinformatics·Marco MasseroliStefano Ceri
Jun 20, 2015·Epilepsy Research·Lynette G SadleirIngrid E Scheffer
Aug 11, 2015·Genome Biology·Britta A M Bouwman, Wouter de Laat
Mar 24, 2015·Nature Methods·Charles G DankoAdam Siepel
Nov 21, 2014·Science·Jeff VierstraJohn A Stamatoyannopoulos
Oct 4, 2014·American Journal of Human Genetics·Wenqing FuJoshua M Akey
Aug 21, 2013·Cell·Andrew B StergachisJohn A Stamatoyannopoulos
Sep 11, 2012·Cell·Shane NephJohn A Stamatoyannopoulos
Sep 2, 2014·Frontiers in Genetics·Iros BarozziMarco J Morelli
Jan 13, 2015·Nature Biotechnology·Mingdong LiuGeorge Stamatoyannopoulos

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