Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format. BCFtools: Reading/writing BCF2/VCF/gVCF files and calling/filtering summarising SNP and short indel sequence variants. HTSlib: A C library for reading/writing high-throughput sequencing data. Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.


References in zbMATH (referenced in 21 articles )

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  1. Pierre Morisse, Claire Lemaitre, Fabrice Legeai: LRez: C++ API and toolkit for analyzing and managing Linked-Reads data (2021) arXiv
  2. Andres Veidenberg, Ari L: Pline: automatic generation of modern web interfaces for command-line programs (2020) arXiv
  3. Robinson, Peter N.; Piro, Rosario Michael; Jäger, Marten: Computational exome and genome analysis (2018)
  4. Wolff, Alexander: Analysis of expression profile and gene variation via development of methods for next generation sequencing data (2018)
  5. Barturen, Guillermo; Oliver, José L.; Hackenberg, Michael: Error correction in methylation profiling from NGS bisulfite protocols (2017)
  6. Benoit, Gaetan; Lemaitre, Claire; Rizk, Guillaume; Drezen, Erwan; Lavenier, Dominique: De novo NGS data compression (2017)
  7. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  8. Liu, Yongchao; Schmidt, Bertil: CUSHAW suite: parallel and efficient algorithms for NGS read alignment (2017)
  9. Shomroni, Orr: Development of algorithms and next-generation sequencing data workflows for the analysis of gene regulatory networks (2017)
  10. Weese, David; Siragusa, Enrico: Full-text indexes for high-throughput sequencing (2017)
  11. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  12. Dallard, Clément; Weller, Mathias; Chateau, Annie; Giroudeau, Rodolphe: Instance guaranteed ratio on greedy heuristic for genome scaffolding (2016)
  13. Lee, Juhee; Müller, Peter; Gulukota, Kamalakar; Ji, Yuan: A Bayesian feature allocation model for tumor heterogeneity (2015)
  14. Lawrence, Michael; Morgan, Martin: Scalable genomics with \textttRand bioconductor (2014)
  15. Zhao, Zhigen; Wang, Wei; Wei, Zhi: An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data (2013)
  16. Giancarlo, R.; Scaturro, D.; Utro, F.: Textual data compression in computational biology: algorithmic techniques (2012)
  17. Policriti, Alberto; Tomescu, Alexandru I.; Vezzi, Francesco: A randomized numerical aligner (rNA) (2012)
  18. Ryan M. Layer, Ira M. Hall, Aaron R. Quinlan: LUMPY: A probabilistic framework for structural variant discovery (2012) arXiv
  19. Glez-Peña, Daniel; Gómez-López, Gonzalo; Reboiro-Jato, Miguel; Fdez-Riverola, Florentino; Pisano, David G.: Pileline: a toolbox to handle genome position information in next-generation sequencing studies (2011) ioport
  20. De Schrijver, Joachim M.; De Leeneer, Kim; Lefever, Steve; Sabbe, Nick; Pattyn, Filip; Van Nieuwerburgh, Filip; Coucke, Paul; Deforce, Dieter; Vandesompele, Jo; Bekaert, Sofie; Hellemans, Jan; Van Criekinge, Wim: Analysing 454 amplicon resequencing experiments using the modular and database oriented variant identification pipeline (2010) ioport

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