:: DESCRIPTION
RLM is a fast and scalable tool for the computation of frequently used Read-Level Methylation statistics.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Hetzel S, Giesselmann P, Reinert K, Meissner A, Kretzmer H.
RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data.
Bioinformatics. 2021 Oct 2:btab663. doi: 10.1093/bioinformatics/btab663. Epub ahead of print. PMID: 34601556.
:: DESCRIPTION
BStools is a sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites.
::DEVELOPER
:: SCREENSHOTS
N/a
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing.
Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J.
Bioinformatics. 2015 Feb 13. pii: btv089
:: DESCRIPTION
AKSmooth is a statistical method that can accurately and efficiently reconstruct the single CpG methylation estimate across the entire methylome using low-coverage bisulfite sequencing (Bi-Seq) data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Bioinform Comput Biol. 2014 Dec;12(6):1442005. doi: 10.1142/S0219720014420050.
AKSmooth: enhancing low-coverage bisulfite sequencing data via kernel-based smoothing.
Chen J1, Lutsik P, Akulenko R, Walter J, Helms V.
:: DESCRIPTION
GPU-BSM (GPU-BiSulfite reads Mapping) is a GPU-based tool devised to map bisulfite-treated reads.
::DEVELOPER
the National Institute of Biomedical Technologies, The National Research Council (CNR) , Italy
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2014 May 19;9(5):e97277. doi: 10.1371/journal.pone.0097277. eCollection 2014.
GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
Manconi A, Orro A, Manca E, Armano G, Milanesi L
:: DESCRIPTION
BAM_ABS is a tool which simulates a Bayesian model that computes the posterior probability of mapping a multiread to each candidate genomic location, taking advantage of uniquely aligned reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tran H, Wu X, Tithi S, Sun MA, Xie H, Zhang L.
A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads.
PLoS One. 2016 Mar 24;11(3):e0151826. doi: 10.1371/journal.pone.0151826. PMID: 27011215; PMCID: PMC4806927.
:: DESCRIPTION
MethGo is a simple and effective tool designed for the analysis of data from whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data.
Liao WW, Yen MR, Ju E, Hsu FM, Lam L, Chen PY.
BMC Genomics. 2015 Dec 9;16 Suppl 12:S11. doi: 10.1186/1471-2164-16-S12-S11.
:: DESCRIPTION
bsmooth-align (version 0.8.1). This integrates two different pipelines for aligning WGBS data.
bsseq. This is a R package used for smoothing methylation profiles and identifying DMRs.
bsseqData This is an experiment data package for R, containing an example dataset used in the vignettes (chromosome 21 and 22 from 3 normal colon and 3 colon cancer patients).
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2012 Oct 3;13(10):R83.
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Hansen KD1, Langmead B, Irizarry RA.
:: DESCRIPTION
MethylCoder is a single program that takes of bisulfite-treated reads and outputs per-base methylation data. It also includes scripts for analysis and visualization. In addition to a binary output and a SAM alignment file, the direct output of methylcoder is a text file that looks like
::DEVELOPER
Brent Pedersen @ the Fischer Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2011 Sep 1;27(17):2435-6. doi: 10.1093/bioinformatics/btr394. Epub 2011 Jun 30.
MethylCoder: software pipeline for bisulfite-treated sequences.
Pedersen B, Hsieh TF, Ibarra C, Fischer RL.
:: DESCRIPTION
BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2012 Jul 11;13(7):R61. [Epub ahead of print]
Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data.
Liu Y, Siegmund KD, Laird PW, Berman BP.
