MethGo – Analyzing Whole-genome Bisulfite Sequencing data

MethGo

:: 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

Pao-Yang Chen’s Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MethGo

:: 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.

bsmooth-align 0.8.1 – Analyzing Whole Genome Bisulfite Sequencing (WGBS) data

bsmooth-align

:: 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

RafaLab, Hansen Lab

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

 bsmooth-alignbsseq ,bsseqData

:: 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.

GPU-BSM 2.7.0 – BS-treated Reads Mapping Tool

GPU-BSM 2.7.0

:: 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

  • Linux
  • CUDA (release ≥6.0).

:: DOWNLOAD

 GPU-BSM

:: 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

AKSmooth 1.0 – Ajusted Local Kernel Smoothing for Bisulfite Sequencing data

AKSmooth 1.0

:: 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

AKSmooth team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • R

:: DOWNLOAD

 AKSmooth

:: 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.

BStools – Bisulfite Sequencing Tools

BStools

:: 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

Lab of Statistical Genomic & Cancer Bioinformatics

:: SCREENSHOTS

N/a

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 BStools

:: 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

MethylCoder – Bisulfite-treated Sequences

MethylCoder

:: 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 Pedersenthe Fischer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • C Compiler

:: DOWNLOAD

 MethylCoder

:: 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.

Bis-SNP 0.82.2 – Bisulfite Space Genotyper & Methylation Caller

BisSNP 0.82.2

:: 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

USC Epigenome Center

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • java
  • perl 

:: DOWNLOAD

 Bis-SNP

:: 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.