Soap

SOAP: short oligonucleotide alignment program. We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets.


References in zbMATH (referenced in 36 articles , 1 standard article )

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  1. Gog, Simon; Kärkkäinen, Juha; Kempa, Dominik; Petri, Matthias; Puglisi, Simon J.: Fixed block compression boosting in FM-indexes: theory and practice (2019)
  2. Kuhnle, Alan; Mun, Taher; Boucher, Christina; Gagie, Travis; Langmead, Ben; Manzini, Giovanni: Efficient construction of a complete index for pan-genomics read alignment (2019)
  3. Chen, Yangjun; Wu, Yujia: On the string matching with (k) mismatches (2018)
  4. Daykin, Jacqueline W.; Groult, Richard; Guesnet, Yannick; Lecroq, Thierry; Lefebvre, Arnaud; Léonard, Martine; Prieur-Gaston, Élise: A survey of string orderings and their application to the Burrows-Wheeler transform (2018)
  5. Wolff, Alexander: Analysis of expression profile and gene variation via development of methods for next generation sequencing data (2018)
  6. Daykin, Jacqueline W.; Watson, Bruce: Indeterminate string factorizations and degenerate text transformations (2017)
  7. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  8. Shen, Carol; Shen, Tony; Lin, Jimmy: Comparative assessment of alignment algorithms for NGS data: features, considerations, implementations, and future (2017)
  9. Shomroni, Orr: Development of algorithms and next-generation sequencing data workflows for the analysis of gene regulatory networks (2017)
  10. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  11. Mathé, Ewy (ed.); Davis, Sean (ed.): Statistical genomics. Methods and protocols (2016)
  12. Barton, Carl; Flouri, Tomáš; Iliopoulos, Costas S.; Pissis, Solon P.: Global and local sequence alignment with a bounded number of gaps (2015)
  13. Kotsifakos, Alexios; Stefan, Alexandra; Athitsos, Vassilis; Das, Gautam; Papapetrou, Panagiotis: DRESS: dimensionality reduction for efficient sequence search (2015)
  14. Barton, Carl; Iliopoulos, Costas S.; Lee, Inbok; Mouchard, Laurent; Park, Kunsoo; Pissis, Solon P.: Extending alignments with (k)-mismatches and (\ell)-gaps (2014)
  15. Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko: Multi-pattern matching with bidirectional indexes (2014)
  16. Rossell, David; Attolini, Camille Stephan-Otto; Kroiss, Manuel; Stöcker, Almond: Quantifying alternative splicing from paired-end RNA-sequencing data (2014)
  17. Daugelaite, Jurate; O’Driscoll, Aisling; Sleator, Roy D.: An overview of multiple sequence alignments and cloud computing in bioinformatics (2013)
  18. Cox, Anthony J.; Jakobi, Tobias; Rosone, Giovanna; Schulz-Trieglaff, Ole B.: Comparing DNA sequence collections by direct comparison of compressed text indexes (2012)
  19. Giancarlo, R.; Scaturro, D.; Utro, F.: Textual data compression in computational biology: algorithmic techniques (2012)
  20. Iliopoulos, Costas S.; Kourie, Derrick; Mouchard, Laurent; Musombuka, Themba K.; Pissis, Solon P.; de Ridder, Corne: An algorithm for mapping short reads to a dynamically changing genomic sequence (2012)

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