Literature DB >> 22398614

Detecting and annotating genetic variations using the HugeSeq pipeline.

Hugo Y K Lam, Cuiping Pan, Michael J Clark, Phil Lacroute, Rui Chen, Rajini Haraksingh, Maeve O'Huallachain, Mark B Gerstein, Jeffrey M Kidd, Carlos D Bustamante, Michael Snyder.   

Abstract

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Year:  2012        PMID： 22398614      PMCID： PMC4720384          DOI： 10.1038/nbt.2134

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  17 in total

1.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

2.  Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.

Authors:  Stephan J Sanders; A Gulhan Ercan-Sencicek; Vanessa Hus; Rui Luo; Michael T Murtha; Daniel Moreno-De-Luca; Su H Chu; Michael P Moreau; Abha R Gupta; Susanne A Thomson; Christopher E Mason; Kaya Bilguvar; Patricia B S Celestino-Soper; Murim Choi; Emily L Crawford; Lea Davis; Nicole R Davis Wright; Rahul M Dhodapkar; Michael DiCola; Nicholas M DiLullo; Thomas V Fernandez; Vikram Fielding-Singh; Daniel O Fishman; Stephanie Frahm; Rouben Garagaloyan; Gerald S Goh; Sindhuja Kammela; Lambertus Klei; Jennifer K Lowe; Sabata C Lund; Anna D McGrew; Kyle A Meyer; William J Moffat; John D Murdoch; Brian J O'Roak; Gordon T Ober; Rebecca S Pottenger; Melanie J Raubeson; Youeun Song; Qi Wang; Brian L Yaspan; Timothy W Yu; Ilana R Yurkiewicz; Arthur L Beaudet; Rita M Cantor; Martin Curland; Dorothy E Grice; Murat Günel; Richard P Lifton; Shrikant M Mane; Donna M Martin; Chad A Shaw; Michael Sheldon; Jay A Tischfield; Christopher A Walsh; Eric M Morrow; David H Ledbetter; Eric Fombonne; Catherine Lord; Christa Lese Martin; Andrew I Brooks; James S Sutcliffe; Edwin H Cook; Daniel Geschwind; Kathryn Roeder; Bernie Devlin; Matthew W State
Journal:  Neuron       Date:  2011-06-09       Impact factor: 17.173

3.  A map of human genome variation from population-scale sequencing.

Authors:  Gonçalo R Abecasis; David Altshuler; Adam Auton; Lisa D Brooks; Richard M Durbin; Richard A Gibbs; Matt E Hurles; Gil A McVean
Journal:  Nature       Date:  2010-10-28       Impact factor: 49.962

4.  Human non-synonymous SNPs: server and survey.

Authors:  Vasily Ramensky; Peer Bork; Shamil Sunyaev
Journal:  Nucleic Acids Res       Date:  2002-09-01       Impact factor: 16.971

5.  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

Authors:  Kai Ye; Marcel H Schulz; Quan Long; Rolf Apweiler; Zemin Ning
Journal:  Bioinformatics       Date:  2009-06-26       Impact factor: 6.937

6.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

7.  BEDTools: a flexible suite of utilities for comparing genomic features.

Authors:  Aaron R Quinlan; Ira M Hall
Journal:  Bioinformatics       Date:  2010-01-28       Impact factor: 6.937

8.  BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

Authors:  Ken Chen; John W Wallis; Michael D McLellan; David E Larson; Joelle M Kalicki; Craig S Pohl; Sean D McGrath; Michael C Wendl; Qunyuan Zhang; Devin P Locke; Xiaoqi Shi; Robert S Fulton; Timothy J Ley; Richard K Wilson; Li Ding; Elaine R Mardis
Journal:  Nat Methods       Date:  2009-08-09       Impact factor: 28.547

9.  The variant call format and VCFtools.

Authors:  Petr Danecek; Adam Auton; Goncalo Abecasis; Cornelis A Albers; Eric Banks; Mark A DePristo; Robert E Handsaker; Gerton Lunter; Gabor T Marth; Stephen T Sherry; Gilean McVean; Richard Durbin
Journal:  Bioinformatics       Date:  2011-06-07       Impact factor: 6.937

10.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937
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  54 in total

Review 1.  Toward better understanding of artifacts in variant calling from high-coverage samples.

Authors:  Heng Li
Journal:  Bioinformatics       Date:  2014-06-27       Impact factor: 6.937

Review 2.  Structural variation in the sequencing era.

Authors:  Steve S Ho; Alexander E Urban; Ryan E Mills
Journal:  Nat Rev Genet       Date:  2019-11-15       Impact factor: 53.242

3.  Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline.

Authors:  In-Hee Lee; Kyungjoon Lee; Michael Hsing; Yongjoon Choe; Jin-Ho Park; Shu Hee Kim; Justin M Bohn; Matthew B Neu; Kyu-Baek Hwang; Robert C Green; Isaac S Kohane; Sek Won Kong
Journal:  Hum Mutat       Date:  2014-03-06       Impact factor: 4.878

4.  Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.

Authors:  Brian D Piening; Wenyu Zhou; Kévin Contrepois; Hannes Röst; Gucci Jijuan Gu Urban; Tejaswini Mishra; Blake M Hanson; Eddy J Bautista; Shana Leopold; Christine Y Yeh; Daniel Spakowicz; Imon Banerjee; Cynthia Chen; Kimberly Kukurba; Dalia Perelman; Colleen Craig; Elizabeth Colbert; Denis Salins; Shannon Rego; Sunjae Lee; Cheng Zhang; Jessica Wheeler; M Reza Sailani; Liang Liang; Charles Abbott; Mark Gerstein; Adil Mardinoglu; Ulf Smith; Daniel L Rubin; Sharon Pitteri; Erica Sodergren; Tracey L McLaughlin; George M Weinstock; Michael P Snyder
Journal:  Cell Syst       Date:  2018-01-17       Impact factor: 10.304

5.  Fastq2vcf: a concise and transparent pipeline for whole-exome sequencing data analyses.

Authors:  Xiaoyi Gao; Jianpeng Xu; Joshua Starmer
Journal:  BMC Res Notes       Date:  2015-03-08

6.  RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.

Authors:  Miriam Rubio-Camarillo; Gonzalo Gómez-López; José M Fernández; Alfonso Valencia; David G Pisano
Journal:  Bioinformatics       Date:  2013-04-28       Impact factor: 6.937

7.  Mutation spectrum in human colorectal cancers and potential functional relevance.

Authors:  Hongzhuan Yin; Yichao Liang; Zhaopeng Yan; Baolin Liu; Qi Su
Journal:  BMC Med Genet       Date:  2013-03-08       Impact factor: 2.103

8.  WEP: a high-performance analysis pipeline for whole-exome data.

Authors:  Mattia D'Antonio; Paolo D'Onorio De Meo; Daniele Paoletti; Berardino Elmi; Matteo Pallocca; Nico Sanna; Ernesto Picardi; Graziano Pesole; Tiziana Castrignanò
Journal:  BMC Bioinformatics       Date:  2013-04-22       Impact factor: 3.169

9.  Next generation sequencing in cancer research and clinical application.

Authors:  Derek Shyr; Qi Liu
Journal:  Biol Proced Online       Date:  2013-02-13       Impact factor: 3.244

10.  Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes.

Authors:  Jason D Merker; Krishna M Roskin; Dana Ng; Cuiping Pan; Dianna G Fisk; Jasmine J King; Ramona Hoh; Michael Stadler; Lawrence M Okumoto; Parveen Abidi; Rhonda Hewitt; Carol D Jones; Linda Gojenola; Michael J Clark; Bing Zhang; Athena M Cherry; Tracy I George; Michael Snyder; Scott D Boyd; James L Zehnder; Andrew Z Fire; Jason Gotlib
Journal:  Haematologica       Date:  2013-07-19       Impact factor: 11.047
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