Mosdepth: quick coverage calculation for genomes and exomes.
Mosdepth: quick coverage calculation for genomes and exomes.
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DOI：
10.1093/bioinformatics/btx699
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发表时间：
2018-03-01
期刊：
影响因子：
--
通讯作者：
Quinlan AR
中科院分区：
文献类型：
--
作者：
Pedersen BS;Quinlan AR
Mosdepth是一个新的命令行工具，用于快速计算全基因组测序覆盖率。它测量BAM或CRAM文件中基因组中每个核苷酸位置或基因组区域集合的深度。基因组区域可以指定为BED文件以评估捕获区域的覆盖率，或者指定为拷贝数调用所需的固定大小窗口。Mosdepth使用一种简单的算法，计算效率高，能够快速生成覆盖范围摘要。我们证明了mosdepth比现有的工具更快，并提供了灵活性的覆盖配置文件的类型。 mosdepth可以在MIT许可下从https://github.com/brentp/mosdepth获得。 补充数据可在Bioinformatics在线获得。
Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at either each nucleotide position in a genome or for sets of genomic regions. Genomic regions may be specified as either a BED file to evaluate coverage across capture regions, or as a fixed-size window as required for copy-number calling. Mosdepth uses a simple algorithm that is computationally efficient and enables it to quickly produce coverage summaries. We demonstrate that mosdepth is faster than existing tools and provides flexibility in the types of coverage profiles produced. mosdepth is available from https://github.com/brentp/mosdepth under the MIT license. Supplementary data are available at Bioinformatics online.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
64.8
作者：
Mallick, Swapan;Li, Heng;Lipson, Mark;Mathieson, Iain;Gymrek, Melissa;Racimo, Fernando;Zhao, Mengyao;Chennagiri, Niru;Nordenfelt, Susanne;Tandon, Arti;Skoglund, Pontus;Lazaridis, Iosif;Sankararaman, Sriram;Fu, Qiaomei;Rohland, Nadin;Renaud, Gabriel;Erlich, Yaniv;Willems, Thomas;Gallo, Carla;Spence, Jeffrey P.;Song, Yun S.;Poletti, Giovanni;Balloux, Francois;van Driem, George;de Knijff, Peter;Romero, Irene Gallego;Jha, Aashish R.;Behar, Doron M.;Bravi, Claudio M.;Capelli, Cristian;Hervig, Tor;Moreno-Estrada, Andres;Posukh, Olga L.;Balanovska, Elena;Balanovsky, Oleg;Karachanak-Yankova, Sena;Sahakyan, Hovhannes;Toncheva, Draga;Yepiskoposyan, Levon;Tyler-Smith, Chris;Xue, Yali;Abdullah, M. Syafiq;Ruiz-Linares, Andres;Beall, Cynthia M.;Di Rienzo, Anna;Jeong, Choongwon;Starikovskaya, Elena B.;Metspalu, Ene;Parik, Juri;Villems, Richard;Henn, Brenna M.;Hodoglugil, Ugur;Mahley, Robert;Sajantila, Antti;Stamatoyannopoulos, George;Wee, Joseph T. S.;Khusainova, Rita;Khusnutdinova, Elza;Litvinov, Sergey;Ayodo, George;Comas, David;Hammer, Michael F.;Kivisild, Toomas;Klitz, William;Winkler, Cheryl A.;Labuda, Damian;Bamshad, Michael;Jorde, Lynn B.;Tishkoff, Sarah A.;Watkins, W. Scott;Metspalu, Mait;Dryomov, Stanislav;Sukernik, Rem;Singh, Lalji;Thangaraj, Kumarasamy;Paeaebo, Svante;Kelso, Janet;Patterson, Nick;Reich, David
通讯作者：
Reich, David
影响因子：
9.2
作者：
Pedersen, Brent S.;Collins, Ryan L.;Quinlan, Aaron R.
通讯作者：
Quinlan, Aaron R.
DOI：
10.1093/bioinformatics/btp352
发表时间：
2009-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Handsaker B;Wysoker A;Fennell T;Ruan J;Homer N;Marth G;Abecasis G;Durbin R;1000 Genome Project Data Processing Subgroup
通讯作者：
1000 Genome Project Data Processing Subgroup
影响因子：
--
作者：
Quinlan, Aaron R
通讯作者：
Quinlan, Aaron R