Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
By Felix Krueger, Simon R. Andrews. 2011
4,744 citations recorded by the source corpus.
Summary: A combination of bisulfite treatment of DNA and high-throughput sequencing (BS-Seq) can capture a snapshot of a cell's epigenomic state by revealing its genome-wide cytosine methylation at single base resolution. Bismark is a flexible tool for the time-efficient analysis of BS-Seq data which performs both read mapping and methylation calling in a single convenient step. Its output discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed. Availability and implementation: Bismark is released under the GNU GPLv3+ licence. The source code is freely available from www.bioinformatics.bbsrc.ac.uk/projects/bismark/. Contact: felix.krueger@bbsrc.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Gordon K. Smyth
- Aaron T. L. Lun
- Yunshun Chen
- Kasper D. Hansen
- Christoph Bock
- Lizhong Chen
- Pedro L. Baldoni
- Rafael A. Irizarry
Citations in the corpus
- SDH mutations establish a hypermethylator phenotype in paraganglioma. (2013, positive): “Bisulfite mapping and methylation calling were performed in a single step using the bismark software (Krueger and Andrews, 2011).”
- BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data (2013, positive): “Subsequently, similar tools were developed including Bismark [7], BRAT-BW [8] and MethylCoder [9].”
- methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles (2012, neutral): “Currently, there are two ways that information can be supplied to methylKit:: 1) methylKit can read per base methylation scores from a text file (see Table 1 for an example of such a file); and, 2) methylKit can read SAM format [21] alignments files obtained from Bismark aligner [22].”