Tasuke: a web-based visualization program for large-scale resequencing data

被引:25
作者
Kumagai, Masahiko [1 ]
Kim, Jungsok [1 ]
Itoh, Ryutaro [1 ,2 ]
Itoh, Takeshi [1 ]
机构
[1] Natl Inst Agrobiol Sci, Agrogen Res Ctr, Bioinformat Res Unit, Tsukuba, Ibaraki 3058602, Japan
[2] DYNACOM Co Ltd Chiba, Chiba 2617125, Japan
关键词
FORMAT; GENOME;
D O I
10.1093/bioinformatics/btt295
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Because an enormous amount of sequence data is being collected, a method to effectively display sequence variation information is urgently needed. TASUKE is a web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies and is suitable for rapid data release to the public on the web. The variation and read depths of multiple genomes, as well as annotations, can be shown simultaneously at various scales. We demonstrate the use of TASUKE by applying it to 50 rice and 100 human genome resequencing datasets.
引用
收藏
页码:1806 / 1808
页数:3
相关论文
共 10 条
  • [1] A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
    Cingolani, Pablo
    Platts, Adrian
    Wang, Le Lily
    Coon, Melissa
    Tung Nguyen
    Wang, Luan
    Land, Susan J.
    Lu, Xiangyi
    Ruden, Douglas M.
    [J]. FLY, 2012, 6 (02) : 80 - 92
  • [2] The variant call format and VCFtools
    Danecek, Petr
    Auton, Adam
    Abecasis, Goncalo
    Albers, Cornelis A.
    Banks, Eric
    DePristo, Mark A.
    Handsaker, Robert E.
    Lunter, Gerton
    Marth, Gabor T.
    Sherry, Stephen T.
    McVean, Gilean
    Durbin, Richard
    [J]. BIOINFORMATICS, 2011, 27 (15) : 2156 - 2158
  • [3] Savant: genome browser for high-throughput sequencing data
    Fiume, Marc
    Williams, Vanessa
    Brook, Andrew
    Brudno, Michael
    [J]. BIOINFORMATICS, 2010, 26 (16) : 1938 - 1944
  • [4] Ensembl 2013
    Flicek, Paul
    Ahmed, Ikhlak
    Amode, M. Ridwan
    Barrell, Daniel
    Beal, Kathryn
    Brent, Simon
    Carvalho-Silva, Denise
    Clapham, Peter
    Coates, Guy
    Fairley, Susan
    Fitzgerald, Stephen
    Gil, Laurent
    Garcia-Giron, Carlos
    Gordon, Leo
    Hourlier, Thibaut
    Hunt, Sarah
    Juettemann, Thomas
    Kaehaeri, Andreas K.
    Keenan, Stephen
    Komorowska, Monika
    Kulesha, Eugene
    Longden, Ian
    Maurel, Thomas
    McLaren, William M.
    Muffato, Matthieu
    Nag, Rishi
    Overduin, Bert
    Pignatelli, Miguel
    Pritchard, Bethan
    Pritchard, Emily
    Riat, Harpreet Singh
    Ritchie, Graham R. S.
    Ruffier, Magali
    Schuster, Michael
    Sheppard, Daniel
    Sobral, Daniel
    Taylor, Kieron
    Thormann, Anja
    Trevanion, Stephen
    White, Simon
    Wilder, Steven P.
    Aken, Bronwen L.
    Birney, Ewan
    Cunningham, Fiona
    Dunham, Ian
    Harrow, Jennifer
    Herrero, Javier
    Hubbard, Tim J. P.
    Johnson, Nathan
    Kinsella, Rhoda
    [J]. NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) : D48 - D55
  • [5] Biological Databases at DNA Data Bank of Japan in the Era of Next-Generation Sequencing Technologies
    Kodama, Yuichi
    Kaminuma, Eli
    Saruhashi, Satoshi
    Ikeo, Kazuho
    Sugawara, Hideaki
    Tateno, Yoshio
    Nakamura, Yasukazu
    [J]. ADVANCES IN COMPUTATIONAL BIOLOGY, 2010, 680 : 125 - 135
  • [6] Fast and accurate short read alignment with Burrows-Wheeler transform
    Li, Heng
    Durbin, Richard
    [J]. BIOINFORMATICS, 2009, 25 (14) : 1754 - 1760
  • [7] VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data
    Preston, Mark D.
    Manske, Magnus
    Horner, Neil
    Assefa, Samuel
    Campino, Susana
    Auburn, Sarah
    Zongo, Issaka
    Ouedraogo, Jean-Bosco
    Nosten, Francois
    Anderson, Tim
    Clark, Taane G.
    [J]. BIOINFORMATICS, 2012, 28 (22) : 2983 - 2985
  • [8] Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics
    Sakai, Hiroaki
    Lee, Sung Shin
    Tanaka, Tsuyoshi
    Numa, Hisataka
    Kim, Jungsok
    Kawahara, Yoshihiro
    Wakimoto, Hironobu
    Yang, Ching-chia
    Iwamoto, Masao
    Abe, Takashi
    Yamada, Yuko
    Muto, Akira
    Inokuchi, Hachiro
    Ikemura, Toshimichi
    Matsumoto, Takashi
    Sasaki, Takuji
    Itoh, Takeshi
    [J]. PLANT AND CELL PHYSIOLOGY, 2013, 54 (02) : E6 - +
  • [9] Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
    Thorvaldsdottir, Helga
    Robinson, James T.
    Mesirov, Jill P.
    [J]. BRIEFINGS IN BIOINFORMATICS, 2013, 14 (02) : 178 - 192
  • [10] Xu X., 2011, NAT BIOTECHNOL, V30, P1