Bowtie 2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.


References in zbMATH (referenced in 20 articles )

Showing results 1 to 20 of 20.
Sorted by year (citations)

  1. Bannai, Hideo; Gagie, Travis; I, Tomohiro: Refining the (r)-index (2020)
  2. Marchet, Camille; Lecompte, Lolita; Limasset, Antoine; Bittner, Lucie; Peterlongo, Pierre: A resource-frugal probabilistic dictionary and applications in bioinformatics (2020)
  3. Dobra, Adrian; Valdes, Camilo; Ajdic, Dragana; Clarke, Bertrand; Clarke, Jennifer: Modeling association in microbial communities with clique loglinear models (2019)
  4. Erik Berner Wik; Hampus Olin; Caitlin Vigetun Haughey; Lisa Klasson; Jacques Dainat: GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files (2019) not zbMATH
  5. Blazewicz, Jacek; Kasprzak, Marta; Kierzynka, Michal; Frohmberg, Wojciech; Swiercz, Aleksandra; Wojciechowski, Pawel; Zurkowski, Piotr: Graph algorithms for DNA sequencing -- origins, current models and the future (2018)
  6. Na, Joong Chae; Kim, Hyunjoon; Min, Seunghwan; Park, Heejin; Lecroq, Thierry; Léonard, Martine; Mouchard, Laurent; Park, Kunsoo: FM-index of alignment with gaps (2018)
  7. Barturen, Guillermo; Oliver, José L.; Hackenberg, Michael: Error correction in methylation profiling from NGS bisulfite protocols (2017)
  8. Fiscon, Giulia; Weitschek, Emanuel: String-matching and alignment algorithms for finding motifs in NGS data (2017)
  9. Flouri, Tomáš; Zhang, Jiajie; Czech, Lucas; Kobert, Kassian; Stamatakis, Alexandros: An efficient approach to merging paired-end reads and incorporation of uncertainties (2017)
  10. Gunady, Mohamed K.; Cornwell, Steffen; Mount, Stephen M.; Bravo, Héctor Corrada: Yanagi: transcript segment library construction for RNA-seq quantification (2017)
  11. Kim, Jongkyu; Reinert, Knut: Vaquita: fast and accurate identification of structural variation using combined evidence (2017)
  12. Liu, Yongchao; Schmidt, Bertil: CUSHAW suite: parallel and efficient algorithms for NGS read alignment (2017)
  13. Polishko, Anton; Hasan, Md. Abid; Pan, Weihua; Bunnik, Evelien M.; Le Roch, Karine; Lonardi, Stefano: ThIEF: finding genome-wide trajectories of epigenetics marks (2017)
  14. Schmidt, Markus; Kutzner, Arne; Heese, Klaus: A novel specialized single-linkage clustering algorithm for taxonomically ordered data (2017)
  15. Shen, Carol; Shen, Tony; Lin, Jimmy: Comparative assessment of alignment algorithms for NGS data: features, considerations, implementations, and future (2017)
  16. Theodoridis, Evangelos: Cloud storage-management techniques for NGS data (2017)
  17. Matthew J. Wakefield: Xenomapper: Mapping reads in a mixed species context (2016) not zbMATH
  18. Vroland, Christophe; Salson, Mikaël; Bini, Sébastien; Touzet, Hélène: Approximate search of short patterns with high error rates using the (01^\ast0) lossless seeds (2016)
  19. Wojciechowski, Pawel; Frohmberg, Wojciech; Kierzynka, Michal; Zurkowski, Piotr; Blazewicz, Jacek: G-MAPSEQ -- a new method for mapping reads to a reference genome (2016)
  20. Barton, Carl; Flouri, Tomáš; Iliopoulos, Costas S.; Pissis, Solon P.: Global and local sequence alignment with a bounded number of gaps (2015)