SOCS 2.2 – SOLiD Read Mapper with Bisulfite Sequencing Support

SOCS 2.2

:: DESCRIPTION

SOCS (short oligonucleotide color space) is a SOLiD read mapper with bisulfite sequencing support.SOCS performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. Modes are available for detecting short sequence-space variants (such as SNPs) and for detecting unlimited numbers of bisulfite-induced nucleotide substitutions for 5mC methylation studies.

::DEVELOPER

Nicholas H. Bergman (nickbergman@gatech.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

SOCS

:: MORE INFORMATION

Citation

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.
Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH.
Bioinformatics. 2010 Aug 1;26(15):1901-2. doi: 10.1093/bioinformatics/btq291.

Bis-class v2 – Bisulfite-sequencing data Classification

Bis-class v2

:: DESCRIPTION

Bis-Class is a tool which is made for classifying methylation status from BS-seq data. This method works best especially when whole methylation level is low and coverage is also low.

::DEVELOPER

Bioinformatics and Biostatistics Lab, Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

Bis-Class

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jul 18;15:608. doi: 10.1186/1471-2164-15-608.
Bis-class: a new classification tool of methylation status using bayes classifier and local methylation information.
Huh I, Yang X, Park T1, Yi SV.

WBSA – Bisulfite Sequencing Data Analysis

WBSA

:: DESCRIPTION

WBSA (Web Service for Bisulfite Sequencing Data Analysis) is a free web service for analysis of Whole-Genome Bisulfite-Sequencing (WGBS) and Genome-wide Reduced Representation Bisulfite Sequencing (RRBS) data.

::DEVELOPER

Beijing Institute of Genomics, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PLoS One. 2014 Jan 30;9(1):e86707. doi: 10.1371/journal.pone.0086707. eCollection 2014.
WBSA: web service for bisulfite sequencing data analysis.
Liang F, Tang B, Wang Y, Wang J, Yu C, Chen X, Zhu J, Yan J, Zhao W, Li R.

BiSeq 1.32.0 – Processing and Analyzing Bisulfite Sequencing data

BiSeq 1.32.0

:: DESCRIPTION

The BiSeq (Bisulfite sequencing) package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs).

::DEVELOPER

BiSeq Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R package
BioConductor

:: DOWNLOAD

BiSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1647-53. doi: 10.1093/bioinformatics/btt263. Epub 2013 May 8.
Detection of significantly differentially methylated regions in targeted bisulfite sequencing data.
Hebestreit K, Dugas M, Klein HU.

BSeQC 1.4 – Quality Control of Bisulfite Sequencing Experiments

BSeQC 1.4

:: DESCRIPTION

BSeQC is a quality control package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

BSeQC

:: MORE INFORMATION

Citation

Bioinformatics, 29 (24), 3227-9 2013 Dec 15
BSeQC: Quality Control of Bisulfite Sequencing Experiments
Xueqiu Lin , Deqiang Sun, Benjamin Rodriguez, Qian Zhao, Hanfei Sun, Yong Zhang, Wei Li

LiBis 0.1.5 – An Ultrasensitive Alignment method for low input Bisulfite Sequencing

LiBis 0.1.5

:: DESCRIPTION

LiBis is an integrated Python package for processing low input WGBS data such as cell-free DNA methylome and single-cell DNA methylome sequencing.

::DEVELOPER

Deqiang Sun Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
conda

:: DOWNLOAD

LiBis

:: MORE INFORMATION

MOABS v1.3.8.7 – Model based Analysis of Bisulfite Sequencing data

MOABS v1.3.8.7

:: DESCRIPTION

MOABS is a comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data

::DEVELOPER

Deqiang Sun Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MOABS

:: MORE INFORMATION

Citation:

Genome Biol. 2014 Feb 24;15(2):R38. doi: 10.1186/gb-2014-15-2-r38.
MOABS: model based analysis of bisulfite sequencing data.
Sun D, Xi Y, Rodriguez B, Park HJ, Tong P, Meong M, Goodell MA, Li W.

MethylExtract 1.9.1 – Methylation Maps and SNV calling from Whole Genome Bisulfite Sequencing Data

MethylExtract 1.9.1

:: DESCRIPTION

MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

MethylExtract

:: MORE INFORMATION

Citation

Version 2. F1000Res. 2013 Oct 15 [revised 2014 Feb 21];2:217. doi: 10.12688/f1000research.2-217.v2. eCollection 2013.
MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data.
Barturen G, Rueda A, Oliver JL, Hackenberg M.