Fast gapped-read alignment with Bowtie 2.

Langmead B;Trapnell C;Pop M;Salzberg SL

Li H;Durbin R

Altshuler, David;Durbin, Richard M.;Abecasis, Goncalo R.;Bentley, David R.;Chakravarti, Aravinda;Clark, Andrew G.;Collins, Francis S.;De la Vega, Francisco M.;Donnelly, Peter;Egholm, Michael;Flicek, Paul;Gabriel, Stacey B.;Gibbs, Richard A.;Knoppers, Bartha M.;Lander, Eric S.;Lehrach, Hans;Mardis, Elaine R.;McVean, Gil A.;Nickerson, DebbieA.;Peltonen, Leena;Schafer, Alan J.;Sherry, Stephen T.;Wang, Jun;Wilson, Richard K.;Gibbs, Richard A.;Deiros, David;Metzker, Mike;Muzny, Donna;Reid, Jeff;Wheeler, David;Wang, Jun;Li, Jingxiang;Jian, Min;Li, Guoqing;Li, Ruiqiang;Liang, Huiqing;Tian, Geng;Wang, Bo;Wang, Jian;Wang, Wei;Yang, Huanming;Zhang, Xiuqing;Zheng, Huisong;Lander, Eric S.;Altshuler, David L.;Ambrogio, Lauren;Bloom, Toby;Cibulskis, Kristian;Fennell, Tim J.;Gabriel, Stacey B.;Jaffe, David B.;Shefler, Erica;Sougnez, Carrie L.;Bentley, David R.;Gormley, Niall;Humphray, Sean;Kingsbury, Zoya;Koko-Gonzales, Paula;Stone, Jennifer;McKernan, Kevin J.;Costa, Gina L.;Ichikawa, Jeffry K.;Lee, Clarence C.;Sudbrak, Ralf;Lehrach, Hans;Borodina, Tatiana A.;Dahl, Andreas;Davydov, Alexey N.;Marquardt, Peter;Mertes, Florian;Nietfeld, Wilfiried;Rosenstiel, Philip;Schreiber, Stefan;Soldatov, Aleksey V.;Timmermann, Bernd;Tolzmann, Marius;Egholm, Michael;Affourtit, Jason;Ashworth, Dana;Attiya, Said;Bachorski, Melissa;Buglione, Eli;Burke, Adam;Caprio, Amanda;Celone, Christopher;Clark, Shauna;Conners, David;Desany, Brian;Gu, Lisa;Guccione, Lorri;Kao, Kalvin;Kebbel, Andrew;Knowlton, Jennifer;Labrecque, Matthew;McDade, Louise;Mealmaker, Craig;Minderman, Melissa;Nawrocki, Anne;Niazi, Faheem;Pareja, Kristen;Ramenani, Ravi;Riches, David;Song, Wanmin;Turcotte, Cynthia;Wang, Shally;Mardis, Elaine R.;Dooling, David;Fulton, Lucinda;Fulton, Robert;Weinstock, George;Durbin, Richard M.;Burton, John;Carter, David M.;Churcher, Carol;Coffey, Alison;Cox, Anthony;Palotie, Aarno;Quail, Michael;Skelly, Tom;Stalker, James;Swerdlow, Harold P.;Turner, Daniel;De Witte, Anniek;Giles, Shane;Gibbs, Richard A.;Wheeler, David;Bainbridge, Matthew;Challis, Danny;Sabo, Aniko;Yu, Fuli;Yu, Jin;Wang, Jun;Fang, Xiaodong;Guo, Xiaosen;Li, Ruiqiang;Li, Yingrui;Luo, Ruibang;Tai, Shuaishuai;Wu, Honglong;Zheng, Hancheng;Zheng, Xiaole;Zhou, Yan;Yang, Huanming;Marth, Gabor T.;Garrison, Erik P.;Huang, Weichun;Indap, Amit;Kural, Deniz;Lee, Wan-Ping;Leong, Wen Fung;Huang, Weichun;Indap, Amit;Kural, Deniz;Lee, Wan-Ping;Leong, Wen Fung;Quinlan, Aaron R.;Stewart, Chip;Stromberg, Michael P.;Ward, Alistair N.;Wu, Jiantao;Lee, Charles;Mills, Ryan E.;Shi, Xinghua;Daly, Mark J.;DePristo, Mark A.;Altshuler, David L.;Ball, Aaron D.;Banks, Eric;Bloom, Toby;Browning, Brian L.;Cibulskis, Kristian;Fennell, Tim J.;Garimella, Kiran V.;Grossman, Sharon R.;Handsaker, Robert E.;Hanna, Matt;Hartl, Chris;Jaffe, David B.;Kernytsky, Andrew M.;Korn, Joshua M.;Li, Heng;Maguire, Jared R.;McCarroll, Steven A.;McKenna, Aaron;Nemesh, James C.;Philippakis, Anthony A.;Poplin, Ryan E.;Price, Alkes;Rivas, Manuel A.;Sabeti, Pardis C.;Schaffner, Stephen F.;Shefler, Erica;Shlyakhter, Ilya A.;Cooper, David N.;Ball, Edward V.;Mort, Matthew;Phillips, Andrew D.;Stenson, Peter D.;Sebat, Jonathan;Makarov, Vladimir;Ye, Kenny;Yoon, Seungtai C.;Bustamante, Carlos D.;Clark, Andrew G.;Boyko, Adam;Degenhardt, Jeremiah;Gravel, Simon;Gutenkunst, Ryan N.;Kaganovich, Mark;Keinan, Alon;Lacroute, Phil;Ma, Xia;Reynolds, Andy;Clarke, Laura;Flicek, Paul;Cunningham, Fiona;Herrero, Javier;Keenen, Stephen;Kulesha, Eugene;Leinonen, Rasko;McLaren, WilliamM.;Radhakrishnan, Rajesh;Smith, Richard E.;Zalunin, Vadim;Zheng-Bradley, Xiangqun;Korbel, Jan O.;Stuetz, Adrian M.;Humphray, Sean;Bauer, Markus;Cheetham, R. Keira;Cox, Tony;Eberle, Michael;James, Terena;Kahn, Scott;Murray, Lisa;Ye, Kai;De La Vega, Francisco M.;Fu, Yutao;Hyland, Fiona C. L.;Manning, Jonathan M.;McLaughlin, Stephen F.;Peckham, Heather E.;Sakarya, Onur;Sun, Yongming A.;Tsung, Eric F.;Batzer, Mark A.;Konkel, Miriam K.;Walker, Jerilyn A.;Sudbrak, Ralf;Albrecht, Marcus W.;Amstislavskiy, Vyacheslav S.;Herwig, Ralf;Parkhomchuk, Dimitri V.;Sherry, Stephen T.;Agarwala, Richa;Khouri, Hodam.;Morgulis, Aleksandr O.;Paschall, Justin E.;Phan, Lon D.;Rotmistrovsky, Kirill E.;Sanders, Robert D.;Shumway, Martin F.;Xiao, Chunlin;McVean, Gil A.;Auton, Adam;Iqbal, Zamin;Lunter, Gerton;Marchini, Jonathan L.;Moutsianas, Loukas;Myers, Simon;Tumian, Afidalina;Desany, Brian;Knight, James;Winer, Roger;Craig, David W.;Beckstrom-Sternberg, Steve M.;Christoforides, Alexis;Kurdoglu, Ahmet A.;Pearson, Johnv.;Sinari, Shripad A.;Tembe, Waibhav D.;Haussler, David;Hinrichs, Angie S.;Katzman, Sol J.;Kern, Andrew;Kuhn, Robert M.;Przeworski, Molly;Hernandez, Ryan D.;Howie, Bryan;Kelley, Joanna L.;Melton, S. Cord;Abecasis, Goncalo R.;Li, Yun;Anderson, Paul;Blackwell, Tom;Chen, Wei;Cookson, William O.;Ding, Jun;Kang, Hyun Min;Lathrop, Mark;Liang, Liming;Moffatt, Miriam F.;Scheet, Paul;Sidore, Carlo;Snyder, Matthew;Zhan, Xiaowei;Zoellner, Sebastian;Awadalla, Philip;Casals, Ferran;Idaghdour, Youssef;Keebler, John;Stone, Eric A.;Zilversmit, Martine;Jorde, Lynn;Xing, Jinchuan;Eichler, Evan E.;Aksay, Gozde;Alkan, Can;Hajirasouliha, Iman;Hormozdiari, Fereydoun;Kidd, Jeffrey M.;Sahinalp, S. Cenk;Sudmant, Peter H.;Mardis, Elaine R.;Chen, Ken;Chinwalla, Asif;Ding, Li;Koboldt, Daniel C.;McLellan, Mike D.;Dooling, David;Weinstock, George;Wallis, John W.;Wendl, Michael C.;Zhang, Qunyuan;Durbin, Richard M.;Albers, Cornelis A.;Ayub, Qasim;Balasubramaniam, Senduran;Barrett, Jeffrey C.;Carter, David M.;Chen, Yuan;Conrad, Donald F.;Danecek, Petr;Dermitzakis, Emmanouil T.;Hu, Min;Huang, Ni;Hurles, Matt E.;Jin, Hanjun;Jostins, Luke;Keane, Thomas M.;Keane, Thomas M.;Le, Si Quang;Lindsay, Sarah;Long, Quan;MacArthur, Daniel G.;Montgomery, Stephen B.;Parts, Leopold;Stalker, James;Tyler-Smith, Chris;Walter, Klaudia;Zhang, Yujun;Gerstein, Mark B.;Snyder, Michael;Abyzov, Alexej;Abyzov, Alexej;Balasubramanian, Suganthi;Bjornson, Robert;Du, Jiang;Grubert, Fabian;Habegger, Lukas;Haraksingh, Rajini;Jee, Justin;Khurana, Ekta;Lam, Hugo Y. K.;Leng, Jing;Mu, Xinmeng Jasmine;Urban, Alexander E.;Zhang, Zhengdong;Li, Yingrui;Luo, Ruibang;Marth, Gabor T.;Garrison, Erik P.;Kural, Deniz;Quinlan, Aaron R.;Stewart, Chip;Stromberg, Michael P.;Ward, Alistair N.;Wu, Jiantao;Lee, Charles;Mills, Ryan E.;Shi, Xinghua;McCarroll, Steven A.;Banks, Eric;DePristo, Mark A.;Handsaker, Robert E.;Hartl, Chris;Korn, Joshua M.;Li, Heng;Nemesh, James C.;Sebat, Jonathan;Makarov, Vladimir;Ye, Kenny;Yoon, Seungtai C.;Degenhardt, Jeremiah;Kaganovich, Mark;Clarke, Laura;Smith, Richard E.;Zheng-Bradley, Xiangqun;Korbel, Jan O.;Humphray, Sean;Cheetham, R. Keira;Eberle, Michael;Kahn, Scott;Murray, Lisa;Ye, Kai;De la Vega, Francisco M.;Fu, Yutao;Peckham, Heather E.;Sun, Yongming A.;Batzer, Mark A.;Konkel, Miriam K.;Xiao, Chunlin;Iqbal, Zamin;Desany, Brian;Blackwell, Tom;Snyder, Matthew;Xing, Jinchuan;Eichler, Evan E.;Aksay, Gozde;Alkan, Can;Hajirasouliha, Iman;Hormozdiari, Fereydoun;Kidd, Jeffrey M.;Chen, Ken;Chinwalla, Asif;Ding, Li;McLellan, Mike D.;Wallis, John W.;Hurles, Matt E.;Conrad, Donald F.;Walter, Klaudia;Zhang, Yujun;Gerstein, Mark B.;Snyder, Michael;Abyzov, Alexej;Du, Jiang;Grubert, Fabian;Haraksingh, Rajini;Jee, Justin;Khurana, Ekta;Lam, Hugo Y. K.;Leng, Jing;Mu, Xinmeng Jasmine;Urban, Alexander E.;Zhang, Zhengdong;Gibbs, Richard A.;Bainbridge, Matthew;Challis, Danny;Coafra, Cristian;Dinh, Huyen;Kovar, Christie;Lee, Sandy;Muzny, Donna;Nazareth, Lynne;Reid, Jeff;Sabo, Aniko;Yu, Fuli;Yu, Jin;Marth, Gabor T.;Garrison, Erik P.;Indap, Amit;Leong, Wen Fung;Quinlan, Aaron R.;Stewart, Chip;Ward, Alistair N.;Wu, Jiantao;Cibulskis, Kristian;Fennell, Tim J.;Gabriel, Stacey B.;Garimella, Kiran V.;Hartl, Chris;Shefler, Erica;Sougnez, Carrie L.;Wilkinson, Jane;Clark, Andrew G.;Gravel, Simon;Grubert, Fabian;Clarke, Laura;Flicek, Paul;Smith, Richard E.;Zheng-Bradley, Xiangqun;Sherry, Stephen T.;Khouri, Hoda M.;Paschall, Justin E.;Shumway, Martin F.;Xiao, Chunlin;McVean, Gil A.;Katzman, Sol J.;Abecasis, Goncalo R.;Blackwell, Tom;Mardis, Elaine R.;Dooling, David;Fulton, Lucinda;Fulton, Robert;Koboldt, Daniel C.;Durbin, Richard M.;Balasubramaniam, Senduran;Coffey, Allison;Keane, Thomas M.;MacArthur, Daniel G.;Palotie, Aarno;Scott, Carol;Stalker, James;Tyler-Smith, Chris;Gerstein, Mark B.;Balasubramanian, Suganthi;Chakravarti, Aravinda;Knoppers, Bartha M.;Peltonen, Leena;Abecasis, Goncalo R.;Bustamante, Carlos D.;Gharani, Neda;Gibbs, Richard A.;Jorde, Lynn;Kaye, Jane S.;Kent, Alastair;Li, Taosha;McGuire, Amy L.;McVean, Gil A.;Ossorio, Pilar N.;Rotimi, Charles N.;Su, Yeyang;Toji, Lorraine H.;Tyler-Smith, Chris;Brooks, Lisa D.;Felsenfeld, Adam L.;McEwen, Jean E.;Abdallah, Assya;Juenger, Christopher R.;Clemm, Nicholas C.;Collins, Francis S.;Duncanson, Audrey;Green, Eric D.;Guyer, Mark S.;Peterson, Jane L.;Schafer, Alan J.;Abecasis, Goncalo R.;Altshuler, David L.;Auton, Adam;Brooks, Lisa D.;Durbin, Richard M.;Gibbs, Richard A.;Hurles, Matt E.;McVean, Gil A.

Li, Ruiqiang;Yu, Chang;Wang, Jun