For better experience, turn on JavaScript!


Rbowtie2

Rbowtie2

Rbowtie2 is an R tool that wraps the Bowtie 2 tool and includes adapter removal, read merging and identification.

Topic

Sequencing

Details

  • Operation: Sequence merging
  • Software interface: Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v>=3
  • Cost: Free
  • Version name: 1.8.0
  • Credit: National Science Foundation of China, Tsinghua University Initiative Scientific Research Program, Open Research Fund of State Key Laboratory of Bioelectronics, Southeast University.
  • Contact: Zheng Wei wzweizheng _at_ qq.com
  • Collection: BioConductor

Publications

Wei Z, Zhang W, Fang H, Li Y, Wang X "esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis." Bioinformatics. 2018 Aug 1;34(15):2664-2665. https://doi.org/10.1093/bioinformatics/bty141
PMID: 29522192
PMCID: PMC6061683


Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590


Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600


Download and documentation








If you find errors, please report here.