Mason – A Read Simulator for Second Generation Sequencing Data

Keywords

Computer science, Software, Sanger sequencing, Source code, Data mining

References

• A Dataset Generator for Whole Genome Shotgun SequencingGerald Myers — 1999
• Accurate Whole Human Genome Sequencing using Reversible Terminator ChemistryDavid Bentley, Shankar Balasubramanian, Harold Swerdlow — 2008
• MetaSim—A Sequencing Simulator for Genomics and MetagenomicsDaniel C. Richter, Felix Ott, Alexander F. Auch — 2008
• The Sequence Alignment/Map format and SAMtoolsHeng Li, Bob Handsaker, Alec Wysoker — 2009
• Genome sequencing in microfabricated high-density picolitre reactorsMarcel Margulies, Michael D. Miller, William E. Altman — 2005
• Substantial biases in ultra-short read data sets from high-throughput DNA sequencingJuliane C. Dohm, Claudio Lottaz, Tatiana Borodina — 2008
• A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short readsTobias Rausch, Sergey Koren, Gennady Denisov — 2009
• Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsimSusanne Balzer, Ketil Malde, Anders Lanzén — 2010
• RazerS--fast read mapping with sensitivity control.David Weese, Anne‐Katrin Emde, Tobias Rausch — 2009
• Supplementary Material for “A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping”M. Holtgrewe, Anne-Katrin Emde, D. Weese — 2011

Cited by

• Characteristics of Pyrosequencing Data – Analysis, Methods, and ToolsSusanne Balzer — 2013
• PopAlu: population-scale discovery of Alu polymorphismsYu Qian, Birte Kehr, Bjarni V. Halldórsson — 2015
• New algorithmic and bioinformatic approaches for the analysis of data from high throughput sequencing. (Algorithmes bio-informatiques pour l'analyse de données de séquençage à haut débit)Evguenia Kopylova — 2013
• Next-generation sequencing algorithms: from read mapping to variant detectionAnne‐Katrin Emde — 2013
• Computational methods and graphical models for integrative proteogenomics (Methoden und graphische Modelle für die integrative Proteogenomik)Franziska Zickmann — 2015
• A Long Fragment Aligner called ALFALFAMichaël Vyverman, Bernard De Baets, Veerle Fack — 2015
• BitMapper: an efficient all-mapper based on bit-vector computingHaoyu Cheng, Huaipan Jiang, Jiaoyun Yang — 2015
• Best practices for evaluating single nucleotide variant calling methods for microbial genomicsNathan D. Olson, Steven P. Lund, Rebecca E. Colman — 2015
• Computational methods for the identification and quantification of microbial organisms in metagenomesMartin Lindner — 2014
• Haplotype-based variant detection from short-read sequencingErik Garrison, Gábor Marth — 2012
• SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysisAndrew T. Magis, Cory C. Funk, Nathan D. Price — 2015
• AMAS: Optimizing the Partition and Filtration of Adaptive Seeds to Speed up Read MappingNgoc Hieu Tran, Xin Chen — 2015
• MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphismsFranziska Zickmann, Bernhard Y. Renard — 2015
• MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.Rachamalla Maheedhar Reddy, Monzoorul Haque Mohammed, Sharmila S. Mande — 2014
• PSIM: pattern-based read simulator for RNA-seq analysisSang‐Min Lee, Haesung Tak, Kiejung Park — 2014
• Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory AccessAlejandro Chacón, Santiago Marco‐Sola, Antonio Espinosa — 2015
• PopIns: population-scale detection of novel sequence insertionsBirte Kehr, Páll Melsted, Bjarni V. Halldórsson — 2015
• Lighter: fast and memory-efficient sequencing error correction without countingLi Song, Liliana Florea, Ben Langmead — 2014
• RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNAImogen A. Wright, Simon Travers — 2014
• RNA-Seq Read Simulator Using SAM TemplateSangmin Lee, Haesung Tak, Kiejung Park — 2013

Related papers

• Fast gapped-read alignment with Bowtie 2Ben Langmead, Steven L. Salzberg — 2012
• The Sequence Alignment/Map format and SAMtoolsHeng Li, Bob Handsaker, Alec Wysoker — 2009
• Fast and accurate short read alignment with Burrows–Wheeler transformHeng Li, Richard Durbin — 2009
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeBen Langmead, Cole Trapnell, Mihai Pop — 2009
• Aligning sequence reads, clone sequences and assembly contigs with BWA-MEMHeng Li — 2013
• A fast bit-vector algorithm for approximate string matching based on dynamic programmingGene Myers — 1998
• Mapping short DNA sequencing reads and calling variants using mapping quality scores.Heng Li, Jue Ruan, Richard Durbin — 2008
• ART: a next-generation sequencing read simulatorWeichun Huang, Leping Li, Jason R. Myers — 2012
• Basic local alignment search tool.Stephen F. Altschul, Warren Gish, Webb Miller — 1990
• A novel and well-defined benchmarking method for second generation read mappingManuel Holtgrewe, Anne‐Katrin Emde, David Weese — 2011