Tag short-read [113 articles] Export

Recent papers classified by the tag short-read.

	Short-Read Sequencing Technologies for Transcriptional Analyses [My Copy] Annual Review of Plant Biology, Vol. 60, No. 1. (9 January 2009), pp. 305-333. by Stacey A. Simon, Jixian Zhai, Raja S. Nandety, et al.Kevin P. McCormick, Jia Zeng, Diego Mejia, Blake C. Meyers posted to transcriptome short-read review by n00c on 2009-12-03 14:10:30 as along with 7 people darian giovenko heliopais manduca GeeSharpMinor orzenil abizar
	Assembly of Large Genomes from Paired Short Reads [My Copy] Bioinformatics and Computational Biology In Bioinformatics and Computational Biology (2009), pp. 30-43. by Benjamin Jackson, Patrick Schnable, Srinivas Aluru posted to short-read paired-end genome assembly algorithm by n00c on 2009-12-03 14:02:07 as along with 1 person seb1
	Fragment assembly with short reads. [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 20, No. 13. (1 September 2004), pp. 2067-2074. by Mark Chaisson, Pavel Pevzner, Haixu Tang posted to short-read assembly by n00c on 2009-12-03 13:30:16 as along with 6 people darian idoerg dakelley orzenil bioinfo nedwards
	SHOREmap: simultaneous mapping and mutation identification by deep sequencing [My Copy] Nature Methods, Vol. 6, No. 8. (01 August 2009), pp. 550-551. by Korbinian Schneeberger, Stephan Ossowski, Christa Lanz, et al.Trine Juul, Annabeth H. Petersen, Kare L. Nielsen, Jan-Elo Jorgensen, Detlef Weigel, Stig U. Andersen posted to short-read shoremap shore sequencing mutation mapping by n00c on 2009-12-02 18:10:31 as along with 2 people danmaclean jasontsai
	Extending assembly of short DNA sequences to handle error [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2942-2944. by William R. Jeck, Josephine A. Reinhardt, David A. Baltrus, et al.Matthew T. Hickenbotham, Vincent Magrini, Elaine R. Mardis, Jeffery L. Dangl, Corbin D. Jones posted to vcake tool ssake software short-read assembler by n00c on 2009-12-02 17:51:00 as along with 7 people idoerg floatingpoint natstreet druvus guhjy azazello Neeperando
	Assembling millions of short DNA sequences using SSAKE [My Copy] Bioinformatics, Vol. 23, No. 4. (15 February 2007), pp. 500-501. by Rene L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt posted to tool ssake software short-read assembler by n00c on 2009-12-02 17:49:35 as along with 14 people katholt jbhiatt jsatkosk AaronDarling floatingpoint idoerg caseybrown druvus natstreet azazello iris42 nmohelli Neeperando yoonk
	Simultaneous alignment of short reads against multiple genomes [My Copy] Genome Biology, Vol. 10, No. 9. (17 September 2009), R98. by Korbinian Schneeberger, Jorg Hagmann, Stephan Ossowski, et al.Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel posted to short-read mapping genomemapper genome by n00c on 2009-11-24 23:05:35 as along with 12 people seninp darian maren megraw djkt fstrozzi jamselem justinhjohnson torfinnnome reyez natstreet druvus
	SSAHA: a fast search method for large DNA databases. [My Copy] Genome research, Vol. 11, No. 10. (1 October 2001), pp. 1725-1729. by Z. Ning, A. J. Cox, J. C. Mullikin posted to software short-read mapping by torfinnnome on 2009-11-19 09:44:21 as along with 17 people stharward adthrasher mattwa jmanning2k n00c jmcq APRegier natstreet druvus treangen umit mmartin timflutre bpb j3xucite lp2 dmc
	Mapping Accuracy of Short Reads from Massively Parallel Sequencing and the Implications for Quantitative Expression Profiling [My Copy] PLoS ONE, Vol. 4, No. 7. (28 July 2009), e6323. by Nicola Palmieri, Christian Schlötterer posted to software short-read mapping by torfinnnome on 2009-11-16 14:17:29 as along with 16 people and 3 groups hzoltan darian debasis mqbphcw3 stubrown Thaverkamp PabloMarin jasontsai ThomasDOtto heliopais guhjy cisevol n00c natstreet druvus jbhiatt Journal picks JLab BergmanLab
	Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine [My Copy] PLoS ONE, Vol. 4, No. 8. (20 August 2009), e6669. by Marcus J. Claesson, Orla O'Sullivan, Qiong Wang, et al.Janne Nikkilä, Julian R. Marchesi, Hauke Smidt, Willem M. de Vos, R. Paul Ross, Paul W. O'Toole posted to short-read metagenomics 16s by nnnagara on 2009-11-13 01:57:14 as along with 2 people and 1 group skembel neils iSEEM
	BFAST: An Alignment Tool for Large Scale Genome Resequencing [My Copy] PloS one In PLoS ONE, Vol. 4, No. 11. (11 November 2009), e7767. by Nils Homer, Barry Merriman, Stanley F. Nelson posted to short-read ngs mapping by idonaldson on 2009-11-11 08:32:57 as along with 9 people darian MarkFiers gdb oannes n00c friendpine zwang druvus torfinnnome
	How to map billions of short reads onto genomes [My Copy] Nature Biotechnology, Vol. 27, No. 5. (01 May 2009), pp. 455-457. by Cole Trapnell, Steven L. Salzberg posted to software short-read sequencing mapping by torfinnnome on 2009-11-05 12:21:58 as along with 30 people and 5 groups agbiotec burak cthachuk hzoltan tonamswish heliopais giovenko jfr daforerog jonilaserson mkiyer Annab darian polivares ghattem kiekyon n00c GeeSharpMinor guhjy nuin reyez orzenil Thaverkamp natstreet druvus fenghezi Stew inesdesantiago idonaldson neils Bioinformatics Chinnaiyan Lab BergmanLab SIMR bioinformatics Bioinformatics - CRUK
	Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 21. (1 November 2009), pp. 2865-2871. by Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, Zemin Ning posted to software short-read paired-end indels deletions by torfinnnome on 2009-11-03 14:18:02 as along with 6 people darian dakelley n00c natstreet druvus vplagnol
	The Sequence Alignment/Map format and SAMtools [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2078-2079. by Heng Li, Bob Handsaker, Alec Wysoker, et al.Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup posted to viewer short-read by seb1 on 2009-11-02 21:43:21 as along with 28 people and 2 groups n00c darian cthachuk hzoltan heliopais urgi idonaldson GustavoLacerda stubrown cassj kshameer ciax polivares carlosjavierna jandot katholt jmcq guhjy orzenil jasontsai operon farhat AlexBateman chrisamiller nuin natstreet sandfire druvus BergmanLab Journal picks
	The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing [My Copy] Bioinformatics (27 October 2009), btp614. by Nathan L. Clement, Quinn Snell, Mark J. Clement, et al.Peter C. Hollenhorst, Jahnvi Purwar, Barbara J. Graves, Bradley R. Cairns, W. Evan Johnson posted to short-read mapping gnumap algorithm by n00c on 2009-10-28 23:01:09 as along with 4 people darian operon heliopais druvus
	The diploid genome sequence of an Asian individual. [My Copy] Nature, Vol. 456, No. 7218. (6 November 2008), pp. 60-65. by Jun Wang, Wei Wang, Ruiqiang Li, et al.Yingrui Li, Geng Tian, Laurie Goodman, Wei Fan, Junqing Zhang, Jun Li, Juanbin Zhang, Yiran Guo, Binxiao Feng, Heng Li, Yao Lu, Xiaodong Fang, Huiqing Liang, Zhenglin Du, Dong Li, Yiqing Zhao, Yujie Hu, Zhenzhen Yang, Hancheng Zheng, Ines Hellmann, Michael Inouye, John Pool, Xin Yi, Jing Zhao, Jinjie Duan, Yan Zhou, Junjie Qin, Lijia Ma, Guoqing Li, Zhentao Yang, Guojie Zhang, Bin Yang, Chang Yu, Fang Liang, Wenjie Li, Shaochuan Li, Dawei Li, Peixiang Ni, Jue Ruan, Qibin Li, Hongmei Zhu, Dongyuan Liu, Zhike Lu, Ning Li, Guangwu Guo, Jianguo Zhang, Jia Ye, Lin Fang, Qin Hao, Quan Chen, Yu Liang, Yeyang Su, A. San, Cuo Ping, Shuang Yang, Fang Chen, Li Li, Ke Zhou, Hongkun Zheng, Yuanyuan Ren, Ling Yang, Yang Gao, Guohua Yang, Zhuo Li, Xiaoli Feng, Karsten Kristiansen, Gane K. Wong, Rasmus Nielsen, Richard Durbin, Lars Bolund, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang posted to tpgp solexa soap short-read sequence individual-human-genome illumina genome asian by n00c on 2009-10-28 20:16:15 as along with 15 people rshe fenghezi jonilaserson kmdaily daforerog jessopher dakelley vmsr psique GustavoLacerda reyez guhjy caseybrown pkonings djkt
	The need for speed [My Copy] Genome Biology, Vol. 10, No. 3. (2009), 212. by Paul Flicek posted to short-read sequencing mapping by seb1 on 2009-10-28 17:57:08 as along with 3 people and 1 group n00c ghattem druvus SIMR bioinformatics
	ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads [My Copy] Genome Biology, Vol. 10, No. 10. (1 October 2009), R103. by Iain MacCallum, Dariusz Przybylski, Sante Gnerre, et al.Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance Shea, Louise Williams, Sarah Young, Chad Nusbaum, David Jaffe posted to short-read paired-end genome de-brujin bacterial assembly allpaths2 allpaths by n00c on 2009-10-28 13:10:39 as along with 10 people and 1 group djkt azazello dakelley jgill GustavoLacerda ramonvidal justinhjohnson stajich druvus neils Mycology
	RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2615-2616. by Nicole Cloonan, Qinying Xu, Geoffrey J. Faulkner, et al.Darrin F. Taylor, Dave T. P. Tang, Gabriel Kolle, Sean M. Grimmond posted to short-read rna-seq ngs mapping by idonaldson on 2009-10-28 10:21:04 as along with 14 people and 1 group hzoltan cthachuk ethanmj cassj GeeSharpMinor sbmontgomery shyamsg natstreet dswan druvus samgj n00c guhjy GustavoLacerda Journal picks
	De novo transcriptome assembly with ABySS [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2872-2877. by Inanc Birol, Shaun D. Jackman, Cydney B. Nielsen, et al.Jenny Q. Qian, Richard Varhol, Greg Stazyk, Ryan D. Morin, Yongjun Zhao, Martin Hirst, Jacqueline E. Schein, Doug E. Horsman, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, Steven J. M. Jones posted to software short-read sequencing novo de assembly abyss by torfinnnome on 2009-10-26 07:45:22 as along with 10 people n00c dswan dakelley TRHvidsten rtogawa ramonvidal stubrown darshan GustavoLacerda druvus
	TagDust--a program to eliminate artifacts from next generation sequencing data [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2839-2840. by Timo Lassmann, Yoshihide Hayashizaki, Carsten O. Daub posted to short-read ngs mapping artefact by idonaldson on 2009-10-23 16:04:03 as along with 21 people and 1 group darian orzenil hzoltan chvlyl operon kshameer djkt rtogawa seb1 nuin debasis jgill GeeSharpMinor sotacam torfinnnome walshtp heliopais jandot n00c rschulz druvus Journal picks
	Updates to the RMAP short-read mapping software [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2841-2842. by Andrew D. Smith, Wen-Yu Chung, Emily Hodges, et al.Jude Kendall, Greg Hannon, James Hicks, Zhenyu Xuan, Michael Q. Zhang posted to short-read ngs mapping by idonaldson on 2009-10-23 15:59:14 as along with 8 people and 1 group seb1 darian natstreet djkt rtogawa heliopais n00c druvus Journal picks
	A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG) [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2863-2864. by Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. De La Vega posted to short-read ngs mapping by idonaldson on 2009-10-23 15:55:37 as along with 3 people seb1 n00c druvus
	RNA-Seq: a revolutionary tool for transcriptomics. [My Copy] Nature reviews. Genetics, Vol. 10, No. 1. (01 January 2009), pp. 57-63. by Zhong Wang, Mark Gerstein, Michael Snyder posted to short-read rna-seq ngs alternative-splicing alignment by cthachuk on 2009-10-23 00:25:56 as along with 43 people and 1 group bsamal zufar hongkeun_park ngehlenborg hzoltan sandfire maren jwfoley urgi RNA-protein heliopais GustavoLacerda rdiaz TRHvidsten dswan roys woodson8 jonilaserson gdb n00c ThomasDOtto burak natstreet athma druvus tonamswish fishtank daed JohnBallam jmcq dandaman cassj xingxu idonaldson raiyar inesdesantiago vplagnol jbhiatt giovanni orzenil nuin guhjy GeeSharpMinor CUBES
	CloudBurst: highly sensitive read mapping with MapReduce [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1363-1369. by Michael C. Schatz posted to tool short-read ngs mapping by idonaldson on 2009-10-22 09:32:17 as along with 33 people and 2 groups joshdsullivan cthachuk hzoltan jfr walshtp orzenil heliopais dakelley bozdagd agbiotec jandot guhjy n00c cymacs semrich nuin operon AlexBateman fgibson rschulz dswan mitko djkt humburg jmeppley coela vagoskar svenrahmann natstreet brianb Neeperando druvus neils KCL & UCL Bioinformatics Bioinformatics
	Managing and analyzing next-generation sequence data. [My Copy] PLoS computational biology In PLoS Comput Biol, Vol. 5, No. 6. (26 June 2009), e1000369. by Brent G. Richter, David P. Sexton posted to short-read ngs mapping by idonaldson on 2009-10-22 09:25:47 as along with 46 people and 4 groups heliopais jforment jfr burak idoerg Geknitics cthachuk hzoltan chvlyl sameersoi hpaces gdv GeeSharpMinor darian daveGerrard tharris Yanno inesdesantiago jcaddy agbiotec humburg Zephyrus daforerog stubrown GustavoLacerda torfinnnome natstreet polivares orzenil kongl guhjy druvus n00c leemond31 nuin operon jasontsai jmeppley rdiaz michaelbarton dswan reyez kshameer TRHvidsten djkt ppgardne Bioinformatics Core Service BergmanLab Bioinformatics Journal picks
	Slider--maximum use of probability information for alignment of short sequence reads and SNP detection [My Copy] Bioinformatics, Vol. 25, No. 1. (1 January 2009), pp. 6-13. by Nawar Malhis, Yaron S. N. Butterfield, Martin Ester, Steven J. M. Jones posted to software snp short-read sequencing probability mapping illumina alignment by torfinnnome on 2009-10-19 16:06:43 as along with 9 people Julien_Fayolle darian seb1 orzenil jsatkosk n00c mdimon druvus jmeppley
	Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 24. (15 December 2009), pp. 3207-3212. by Jacob F. Degner, John C. Marioni, Athma A. Pai, et al.Joseph K. Pickrell, Everlyne Nkadori, Yoav Gilad, Jonathan K. Pritchard posted to snp short-read masking mapping by torfinnnome on 2009-10-15 15:49:44 as along with 6 people dakelley natstreet chvlyl n00c papamicd heliopais
	Sequencing of natural strains of Arabidopsis thaliana with short reads. [My Copy] Genome research, Vol. 18, No. 12. (29 December 2008), pp. 2024-2033. by Stephan Ossowski, Korbinian Schneeberger, Richard M. Clark, Christa Lanz, Norman Warthmann, Detlef Weigel posted to solexa snp-calling short-read shore sequencing quality pipeline maq illumina error-model arabidopsis by n00c on 2009-10-07 18:05:08 as along with 11 people and 2 groups seninp APRegier sameersoi dandaman jasontsai stajich xwbcn natstreet druvus GustavoLacerda semrich Mycology Notre Dame Bioinformatics
	BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing [My Copy] Genome Research, Vol. 19, No. 10. (6 October 2009), pp. 1884-1895. by Wei-Chun Kao, Kristian Stevens, Yun S. Song posted to short-read pipeline illumina base-calling algorithm by torfinnnome on 2009-10-02 07:53:50 as along with 13 people and 2 groups heliopais dakelley lp2 megraw rdiaz djkt n00c farhat druvus polivares stajich fpattyn jbhiatt BergmanLab Mycology
	De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer [My Copy] Genome Research, Vol. 18, No. 5. (10 May 2008), pp. 802-809. by David Hernandez, Patrice FranÃ§ois, Laurent Farinelli, Magne Ãsterã¥s, Jacques Schrenzel posted to short-read sequencing genome de-novo bacterial assembly by n00c on 2009-10-01 16:16:31 as along with 15 people and 4 groups GeeSharpMinor pachorip operon druvus dakelley acn nmohelli GustavoLacerda jmeppley stajich azazello Katje iris42 balicea Neeperando DeNovoAssembly-SIMR microbiology_nijmegen Mycology gatech-compgenomics
	Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies [My Copy] PLoS ONE, Vol. 2, No. 5. (2007), e484. by Andreas Sundquist, Mostafa Ronaghi, Haixu Tang, Pavel Pevzner, Serafim Batzoglou posted to short-read sequencing assembly by n00c on 2009-10-01 16:14:34 as along with 12 people and 1 group APRegier jessopher natstreet druvus idoerg dakelley GustavoLacerda orzenil guhjy azazello nedwards iris42 gatech-compgenomics
	Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads [My Copy] PLoS Comput Biol In PLoS Comput Biol, Vol. 4, No. 9. (26 September 2008), e1000186. by Steven L. Salzberg, Daniel D. Sommer, Daniela Puiu, Vincent T. Lee posted to short-read genome bacterial assembly assembler by n00c on 2009-09-28 15:27:39 as along with 17 people and 5 groups skembel operon michaelbarton azazello Thaverkamp dakelley sconlan GustavoLacerda treangen natstreet antonkratz druvus vaulot djkt Katje stajich semrich BergmanLab Papers recommended by the Roscoff Plankton Group iSEEM microbiology_nijmegen Mycology
	Short read fragment assembly of bacterial genomes [My Copy] Genome Research, Vol. 18, No. 2. (1 February 2008), pp. 324-330. by Mark J. Chaisson, Pavel A. Pevzner posted to tool software short-read genome eulerian assembly assembler by n00c on 2009-09-28 15:23:30 as along with 17 people pachorip APRegier thegoose2 dakelley Neeperando hpaces idoerg druvus jasontsai acn orzenil azazello GustavoLacerda dandaman caseybrown iris42 tharris
	galign: A Tool for Rapid Genome Polymorphism Discovery [My Copy] PLoS ONE, Vol. 4, No. 9. (25 September 2009), e7188. by Shai Shaham posted to snp short-read illumina discovery annotation by torfinnnome on 2009-09-28 09:29:22 as along with 7 people and 1 group maren scmelton natstreet Benedikt_Zimmermann n00c druvus stajich Mycology
	ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2607-2608. by Martin Morgan, Simon Anders, Michael Lawrence, Patrick Aboyoun, Herve Pages, Robert Gentleman posted to statistics short-read r quality bioconductor by torfinnnome on 2009-09-28 07:55:49 as along with 14 people and 1 group manduca darian jforment fstrozzi rschulz djkt jmeppley dswan walshtp jamesmorris joaocarrico natstreet n00c druvus Bioinformatics Core Service
	Computation of Rank and Select Functions on Hierarchical Binary String and Its Application to Genome Mapping Problems for Short-Read DNA Sequences [My Copy] Journal of Computational Biology (22 September 2009), 090922085727012. by Kouichi Kimura, Yutaka Suzuki, Sumio Sugano, Asako Koike posted to solexa short-read illumina burrows-wheeler algorithm by n00c on 2009-09-23 21:05:06 as along with 3 people seb1 justinhjohnson druvus
	Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing. [My Copy] BMC genomics, Vol. 10, No. 1. (07 June 2009), 259. by Timothy B. Sackton, Andrew G. Clark posted to transcriptome short-read sequencing mosaik cdna by n00c on 2009-09-21 22:44:32 as along with 2 people and 1 group fsm avilella Journal picks
	Fast mapping of short sequences with mismatches, insertions and deletions using index structures. [My Copy] PLoS computational biology, Vol. 5, No. 9. (11 September 2009), e1000502. by Steve Hoffmann, Christian Otto, Stefan Kurtz, et al.Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller posted to tool software short-read segemehl mapping alignment by n00c on 2009-09-11 15:38:04 as along with 19 people and 4 groups cthachuk hzoltan darian nuin fenghezi behindtherabbit jandot walshtp torfinnnome stubrown dswan polivares orzenil natstreet djkt jmcq heliopais ppgardne druvus Bioinformatics BergmanLab iSEEM Journal picks
	A Fast Hybrid Short Read Fragment Assembly Algorithm [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 17. (17 June 2009), pp. btp374-2280. by Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, Simon J. Puglisi posted to short-read assembly by APRegier on 2009-09-02 16:46:27 as along with 16 people and 2 groups torfinnnome hzoltan cthachuk orzenil GustavoLacerda dakelley katholt GeeSharpMinor dayjm djkt dswan pachorip natstreet druvus n00c jmeppley Bioinformatics Journal picks
	Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding [My Copy] Genome Research, Vol. 19, No. 9. (22 September 2009), pp. 1527-1541. by Kevin J. McKernan, Heather E. Peckham, Gina L. Costa, et al.Stephen F. McLaughlin, Yutao Fu, Eric F. Tsung, Christopher R. Clouser, Cisyla Duncan, Jeffrey K. Ichikawa, Clarence C. Lee, Zheng Zhang, Swati S. Ranade, Eileen T. Dimalanta, Fiona C. Hyland, Tanya D. Sokolsky, Lei Zhang, Andrew Sheridan, Haoning Fu, Cynthia L. Hendrickson, Bin Li, Lev Kotler, Jeremy R. Stuart, Joel A. Malek, Jonathan M. Manning, Alena A. Antipova, Damon S. Perez, Michael P. Moore, Kathleen C. Hayashibara, Michael R. Lyons, Robert E. Beaudoin, Brittany E. Coleman, Michael W. Laptewicz, Adam E. Sannicandro, Michael D. Rhodes, Rajesh K. Gottimukkala, Shan Yang, Vineet Bafna, Ali Bashir, Andrew MacBride, Can Alkan, Jeffrey M. Kidd, Evan E. Eichler, Martin G. Reese, Francisco M. De La Vega, Alan P. Blanchard posted to structural solid short-read resequencing human by APRegier on 2009-09-02 16:44:15 as along with 17 people hzoltan gbenson adijr chrisamiller heliopais daforerog druvus djkt psique sameersoi fenghezi jmanning2k xingxu pkonings n00c jandot natstreet
	ALLPATHS: De novo assembly of whole-genome shotgun microreads [My Copy] Genome Research, Vol. 18, No. 5. (13 May 2008), pp. 810-820. by Jonathan Butler, Iain MacCallum, Michael Kleber, et al.Ilya A. Shlyakhter, Matthew K. Belmonte, Eric S. Lander, Chad Nusbaum, David B. Jaffe posted to short-read illumina assembly by APRegier on 2009-08-20 15:43:42 as along with 23 people and 1 group ajsferreira n00c carlk jmanning2k pachorip jonilaserson operon thegoose2 natstreet AaronDarling mhz dakelley druvus stajich azazello hpaces tharris jwhitney iris42 Neeperando sharpton GustavoLacerda GeeSharpMinor Mycology
	SHREC: a short-read error correction method [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2157-2163. by Jan Schroder, Heiko Schroder, Simon J. Puglisi, Ranjan Sinha, Bertil Schmidt posted to short-read sequencing java filtering by torfinnnome on 2009-08-20 10:49:56 as along with 13 people and 1 group heliopais adthrasher dakelley skembel thegoose katholt sotacam djkt rtogawa natstreet druvus n00c jmeppley Journal picks
	PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 19. (1 October 2009), pp. 2514-2521. by Yangho Chen, Tade Souaiaia, Ting Chen posted to spaced-seeds solid short-read seed perm mapping color-space abi by n00c on 2009-08-15 15:42:05 as along with 10 people and 1 group Julien_Fayolle heliopais darian dswan operon fishtank polivares torfinnnome druvus natstreet BergmanLab
	LookSeq: A browser-based viewer for deep sequencing data [My Copy] Genome Research, Vol. 19, No. 11. (29 November 2009), pp. 2125-2132. by Heinrich M. Manske, Dominic P. Kwiatkowski posted to visualization viewer software short-read sequencing resequencing lookseq by n00c on 2009-08-14 21:47:57 as along with 27 people and 2 groups hzoltan darian dakelley tonamswish inesdesantiago Thaverkamp idonaldson heliopais owhitney GustavoLacerda ngehlenborg sandfire fpattyn xianjun katholt stubrown orzenil operon guhjy kongl stajich torfinnnome nuin kshameer neils druvus natstreet BergmanLab Mycology
	High-throughput genotyping by whole-genome resequencing. [My Copy] Genome research, Vol. 19, No. 6. (6 June 2009), pp. 1068-1076. by Xuehui Huang, Qi Feng, Qian Qian, et al.Qiang Zhao, Lu Wang, Ahong Wang, Jianping Guan, Danlin Fan, Qijun Weng, Tao Huang, Guojun Dong, Tao Sang, Bin Han posted to pf454-paper plants resequencing short-read snps by APRegier on 2009-08-10 16:27:17 as along with 9 people jandot n00c reyez sandfire djkt natstreet jbhiatt GeeSharpMinor langmead
	Velvet: Algorithms for de novo short read assembly using de Bruijn graphs [My Copy] Genome Research In Genome Research, Vol. 18, No. 5. (18 May 2008), pp. 821-829. by Daniel R. Zerbino, Ewan Birney posted to assembly illumina short-read by APRegier on 2009-08-07 22:03:46 as along with 42 people and 3 groups ajsferreira vplagnol bedo jwhitney cthachuk hzoltan azazello ajbattle jmanning2k n00c carlk pachorip jbhiatt jonilaserson operon jahwa jsatkosk sandfire thegoose2 katholt robsyme djkt hpaces AaronDarling mhz idoerg jmcq dswan dakelley jasontsai acn druvus natstreet nmohelli stajich farhat iris42 tharris Neeperando sharpton GustavoLacerda gdb Bioinformatics DeNovoAssembly-SIMR Mycology
	A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 30. (25 July 2006), pp. 11240-11245. by Susanne M. D. Goldberg, Justin Johnson, Dana Busam, et al.Tamara Feldblyum, Steve Ferriera, Robert Friedman, Aaron Halpern, Hoda Khouri, Saul A. Kravitz, Federico M. Lauro, Kelvin Li, Yu-Hui Rogers, Robert Strausberg, Granger Sutton, Luke Tallon, Torsten Thomas, Eli Venter, Marvin Frazier, J. Craig Venter posted to 454 assembly pf454-paper short-read by APRegier on 2009-08-07 21:32:53 as along with 8 people and 5 groups justinhjohnson bjorns balicea dchughes azazello beatrizfernandez GustavoLacerda xingxu DeNovoAssembly-SIMR G4ID Microbial-Ecology Genetics-of-Gambling MBLAB
	Genome assembly reborn: recent computational challenges [My Copy] Brief Bioinform, Vol. 10, No. 4. (1 July 2009), pp. 354-366. by Mihai Pop posted to assembly pf454-paper short-read by APRegier on 2009-08-07 20:37:40 as along with 30 people and 1 group jfr hzoltan cthachuk GustavoLacerda n00c agbiotec shabhonam pachorip jmcq stevebs jonilaserson michaelbarton inesdesantiago GeeSharpMinor bertelsen aprasad ananta_samudra sandfire jmeppley mlangill fgibson ppgardne TRHvidsten pengchy robsyme nuin kiekyon natstreet druvus idoerg Journal picks
	Bioinformatics challenges of new sequencing technology [My Copy] Trends in Genetics, Vol. 24, No. 3. (11 February 2008), pp. 142-149. by M. Pop, S. Salzberg posted to assembly pf454-paper review short-read by APRegier on 2009-08-07 20:35:24 as along with 36 people Jporci cthachuk hzoltan hpaces heliopais imaginatio operon daforerog n00c ptrobajo orzenil katholt michaelbarton kiekyon thegoose2 xingxu floatingpoint polivares yupu treangen jmcq delenickphd giovenko jmeppley dchughes djkt GustavoLacerda niallhaslam urgi Neeperando jfr tharris mariakmejia caseybrown yoonk druvus

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mapping	58
software	33
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sequencing	27
tool	19
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rna-seq	16
illumina	15
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ngs	14
resequencing	13
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review	9
assembler	8
solexa	8
de-novo	6
pf454-paper	6
snp	6
transcriptome	6
jennifer-beane	5
solid	5
base-calling	4
burrows-wheeler	4
comparison	4
error-model	4
microarray	4
paired-end	4
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454	3
abi	3
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color-space	3
error	3
maq	3
multiplexing	3
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quality	3
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soap	3
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bioconductor	2
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design	2
durbin	2
li	2
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r	2
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shore	2
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ssake	2
structural	2
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validation	2
viewer	2
16s	1
allpaths	1
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analysis	1
bayescall	1
bwa	1
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de	1
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