TY - JOUR AU - Dijk, E. L. AU - Auger, H. AU - Jaszczyszyn, Y. AU - Thermes, C. PY - 2014 DA - 2014// TI - Ten years of next-generation sequencing technology JO - Trends Genet. VL - 30 UR - https://doi.org/10.1016/j.tig.2014.07.001 DO - 10.1016/j.tig.2014.07.001 ID - Dijk2014 ER - TY - JOUR AU - Soon, W. W. AU - Hariharan, M. AU - Snyder, M. P. PY - 2013 DA - 2013// TI - High-throughput sequencing for biology and medicine JO - Mol Syst Biol. VL - 9 UR - https://doi.org/10.1038/msb.2012.61 DO - 10.1038/msb.2012.61 ID - Soon2013 ER - TY - JOUR AU - Fonseca, N. A. AU - Rung, J. AU - Brazma, A. AU - Marioni, J. C. PY - 2012 DA - 2012// TI - Tools for mapping high-throughput sequencing data JO - Bioinformatics. VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts605 DO - 10.1093/bioinformatics/bts605 ID - Fonseca2012 ER - TY - JOUR AU - Degner, J. F. AU - Marioni, J. C. AU - Pai, A. A. AU - Pickrell, J. K. AU - Nkadori, E. AU - Gilad, Y. PY - 2009 DA - 2009// TI - Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp579 DO - 10.1093/bioinformatics/btp579 ID - Degner2009 ER - TY - JOUR AU - Stevenson, K. R. AU - Coolon, J. D. AU - Wittkopp, P. J. PY - 2013 DA - 2013// TI - Sources of bias in measures of allele-specific expression derived from RNA-sequence data aligned to a single reference genome JO - BMC Genomics. VL - 14 UR - https://doi.org/10.1186/1471-2164-14-536 DO - 10.1186/1471-2164-14-536 ID - Stevenson2013 ER - TY - JOUR AU - Hatem, A. AU - Bozdag, D. AU - Toland, A. E. AU - Catalyurek, U. V. PY - 2013 DA - 2013// TI - Benchmarking short sequence mapping tools JO - BMC Bioinformatics. VL - 14 UR - https://doi.org/10.1186/1471-2105-14-184 DO - 10.1186/1471-2105-14-184 ID - Hatem2013 ER - TY - JOUR AU - Caboche, S. AU - Audebert, C. AU - Lemoine, Y. AU - Hot, D. PY - 2014 DA - 2014// TI - Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data JO - BMC Genomics. VL - 15 UR - https://doi.org/10.1186/1471-2164-15-264 DO - 10.1186/1471-2164-15-264 ID - Caboche2014 ER - TY - JOUR AU - Highnam, G. AU - Wang, J. J. AU - Kusler, D. AU - Zook, J. AU - Vijayan, V. AU - Leibovich, N. PY - 2015 DA - 2015// TI - An analytical framework for optimizing variant discovery from personal genomes JO - Nat Commun. VL - 6 UR - https://doi.org/10.1038/ncomms7275 DO - 10.1038/ncomms7275 ID - Highnam2015 ER - TY - STD TI - dwgsim. Available at: http://sourceforge.net/projects/dnaa. Accessed March 2015 UR - http://sourceforge.net/projects/dnaa ID - ref9 ER - TY - BOOK AU - Holtgrewe, M. PY - 2010 DA - 2010// TI - Mason-A Read Simulator for Second Generation Sequencing Data PB - Institut für Mathematik und Informatik, Freie Universität Berlin CY - Berlin ID - Holtgrewe2010 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. PY - 2009 DA - 2009// TI - The Sequence Alignment/Map format and SAMtools JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with Burrows-Wheeler transform JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - STD TI - Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv e-prints. 2013. ID - ref13 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2010 DA - 2010// TI - Fast and accurate long-read alignment with Burrows-Wheeler transform JO - Bioinformatics. VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp698 DO - 10.1093/bioinformatics/btp698 ID - Li2010 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods. VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Sedlazeck, F. J. AU - Rescheneder, P. AU - Haeseler, A. PY - 2013 DA - 2013// TI - NextGenMap: fast and accurate read mapping in highly polymorphic genomes JO - Bioinformatics. VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt468 DO - 10.1093/bioinformatics/btt468 ID - Sedlazeck2013 ER - TY - JOUR AU - Ruffalo, M. AU - LaFramboise, T. AU - Koyuturk, M. PY - 2011 DA - 2011// TI - Comparative analysis of algorithms for next-generation sequencing read alignment JO - Bioinformatics. VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr477 DO - 10.1093/bioinformatics/btr477 ID - Ruffalo2011 ER - TY - JOUR AU - Phillippy, A. M. AU - Schatz, M. C. AU - Pop, M. PY - 2008 DA - 2008// TI - Genome assembly forensics: finding the elusive mis-assembly JO - Genome Biol. VL - 9 UR - https://doi.org/10.1186/gb-2008-9-3-r55 DO - 10.1186/gb-2008-9-3-r55 ID - Phillippy2008 ER -