One important step in calling methylation of a genome is to map bisulfite reads. Mapping of bisulfite reads is different from that of ChIP-Seq and RNA-Seq data since the non-methylated Cs are converted to Ts by bisulfite treatment and subsequent PCR. The bisulfite reads are…
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Bismark
Desktop

Bismark

A software package to map and determine the methylation state of BS-Seq reads.…

A software package to map and determine the methylation state of BS-Seq reads. Bismark is easy to use, very flexible and is the first published BS-Seq aligner to seamlessly handle single- and…

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GSNAP
Desktop

GSNAP

Aligns both single- and paired-end reads as short as 14 nt and of arbitrarily…

Aligns both single- and paired-end reads as short as 14 nt and of arbitrarily long length. GSNAP can detect short- and long-distance splicing, including interchromosomal splicing, in individual…

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PASS
Desktop

PASS

Aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying…

Aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands. The output of…

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BSMAP
Desktop

BSMAP Bisulfite Sequence Mapping Program

A short reads mapping software tool for bisulfite sequencing reads. BSMAP…

A short reads mapping software tool for bisulfite sequencing reads. BSMAP combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. Compared with existing bisulfite…

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BS Seeker
Desktop
Web

BS Seeker

Provides fast and accurate mapping of bisulfite-converted reads. BS-Seeker2 is…

Provides fast and accurate mapping of bisulfite-converted reads. BS-Seeker2 is an updated version of BS Seeker, as a full pipeline for mapping bisulfite sequencing data and generating DNA methylomes.…

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BatMeth
Desktop

BatMeth

An efficient and accurate general-purpose bisulfite sequence mapping program.…

An efficient and accurate general-purpose bisulfite sequence mapping program. BatMeth can be deployed for the analysis of genome-wide bisulfite sequencing using either base reads or color reads. It…

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MethylCoder
Desktop

MethylCoder

Generates per-base methylation data given a set of bisulfite-treated reads.…

Generates per-base methylation data given a set of bisulfite-treated reads. MethylCoder provides the option to use either of two existing short-read aligners, each with different strengths. It…

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MethPipe
Desktop

MethPipe

A computational pipeline for analyzing bisulfite sequencing data (WGBS and…

A computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS). MethPipe is a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of…

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BRAT
Desktop

BRAT Bisulfite-treated Reads Analysis Tool

An accurate and efficient tool for mapping short reads obtained from the…

An accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. BRAT supports single and paired-end reads and handles input…

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RRBSMAP
Desktop

RRBSMAP

A specifically designed version of BSMAP for reduced representation bisulfite…

A specifically designed version of BSMAP for reduced representation bisulfite sequencing (RRBS).

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Segemehl
Desktop

Segemehl

A tool to map short sequencer reads to reference genomes.

A tool to map short sequencer reads to reference genomes.

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SAAP-RRBS
Desktop

SAAP-RRBS Streamlined Analysis and Annotation Pipeline for RRBS data

Integrates read quality assessment/clean-up, alignment, methylation data…

Integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting and visualization. SAAP-RRBS facilitates a rapid transition from sequencing reads to a fully…

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Pash
Desktop

Pash

Performs sequence comparison and read mapping and can be employed as a module…

Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite…

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ERNE
Desktop

ERNE Extended Randomized Numerical alignEr

A short string alignment package whose goal is to provide an all-inclusive set…

A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE 2 (a.k.a. bw-erne) uses the Burrows Wheeler Transformation (BWT) to…

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SOCS
Desktop

SOCS

Performs ungapped alignment of SOLiD (color space) sequencing reads against…

Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences.

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B-SOLANA
Desktop

B-SOLANA

An approach for the analysis of two-base encoding bisulfite sequencing data.

An approach for the analysis of two-base encoding bisulfite sequencing data.

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GNUMAP-BS
Desktop

GNUMAP-BS

A probabilistic algorithm that addresses the computational problems associated…

A probabilistic algorithm that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome.

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Bison
Desktop

Bison

A BS-seq aligner which exploits multiple nodes of a computer cluster to speed…

A BS-seq aligner which exploits multiple nodes of a computer cluster to speed up this process and also has increased accuracy. Bison is accompanied by a variety of helper programs and scripts to…

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BRAT-nova
Desktop

BRAT-nova Bisulfite-treated Reads Analysis Tool-nova

A completely rewritten and improved implementation of the mapping tool BRAT-BW…

A completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-seq). BRAT-nova employs a novel space-efficient representation of the genome and…

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LAST-TRAIN
Desktop
Web

LAST-TRAIN

Improves sequence alignment accuracy by inferring substitution and gap scores…

Improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. LAST-TRAIN uses a standard…

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Bwa-meth
Desktop

Bwa-meth

Aligns bisulfite-treated sequences and compares it to existing aligners. It…

Aligns bisulfite-treated sequences and compares it to existing aligners. It allows indels, local alignments, and it never writes a temporary-file of the reads to disk, instead streaming the in silico…

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WALT
Desktop

WALT Wildcard ALignment Tool

A software tool for mapping whole-genome bisulfite sequencing (WGBS) reads.…

A software tool for mapping whole-genome bisulfite sequencing (WGBS) reads. WALT uses a strategy of hashing periodic spaced seeds, which leads to significant speedup compared with the most efficient…

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BAM-ABS
Desktop

BAM-ABS

A Bayesian model that assigns multireads to their most likely locations based…

A Bayesian model that assigns multireads to their most likely locations based on the posterior probability derived from information hidden in uniquely aligned reads. Analyses of both simulated data…

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SMAP
Desktop

SMAP Streamlined Methylation Analysis Pipeline

A streamlined package to meet the need of extracting multiple types of…

A streamlined package to meet the need of extracting multiple types of information (such as differentially methylated C sites (DMCs), differentially methylated regions (DMRs), single nucleotide…

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BSPAT
Desktop
Web

BSPAT Bisulfite Sequencing Pattern Analysis Tool

A fast online service for analysing co-occurrence methylation patterns in…

A fast online service for analysing co-occurrence methylation patterns in bisulfite sequencing data. BSPAT integrated sequence mapping, quality control and visualized analysis result of co-occurrence…

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BRAT-BW
Desktop

BRAT-BW Bisulfite-treated Reads Analysis Tool-Burrows-Wheeler transform

A fast, accurate and memory-efficient tool that maps bisulfite-treated short…

A fast, accurate and memory-efficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows-Wheeler transform). BRAT-BW is significantly more memory…

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BStools
Desktop

BStools

A sequential trimming-and-retrieving alignment approach for investigating DNA…

A sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites. The method is…

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Methy-Pipe
Desktop

Methy-Pipe

A software tool that not only fulfills the core data analysis requirements…

A software tool that not only fulfills the core data analysis requirements (e.g. sequence alignment, differential methylation analysis, etc.) but also provides useful tools for methylation data…

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GPU-BSM
Desktop

GPU-BSM

A tool able to map bisulfite-treated reads from whole genome bisulfite…

A tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting…

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MethyQA
Desktop

MethyQA

Provides users with a unique insight into the methylation sequencing data they…

Provides users with a unique insight into the methylation sequencing data they are researching. MethyQA allows the users to determine the quality of their data and better prepares them to address the…

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WBSA
Desktop
Web

WBSA Web Service for Bisulfite Sequencing Data Analysis

A free web application for analysis of whole-genome bisulfite-sequencing (WGBS)…

A free web application for analysis of whole-genome bisulfite-sequencing (WGBS) and genome-wide reduced representation bisulfite sequencing (RRBS) data. WBSA not only focuses on CpG methylation, but…

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BSmooth-align
Desktop

BSmooth-align

Alignment of bisulfite sequence reads and tabulation of read-level methylation…

Alignment of bisulfite sequence reads and tabulation of read-level methylation measurements.

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bisReadMapper
Desktop

bisReadMapper

Fast and lightweight package for mapping bisulfite converted DNA sequencing…

Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform.

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BSmapper
Desktop

BSmapper

Sequence mapper for bisulfite sequencing reads for DNA methylation studies.

Sequence mapper for bisulfite sequencing reads for DNA methylation studies.

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HPG-Methyl
Desktop

HPG-Methyl

A software tool that efficiently maps bisulfite sequencing reads on DNA,…

A software tool that efficiently maps bisulfite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows-Wheeler…

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RRBS-Analyser
Web

RRBS-Analyser

A comprehensive genome-scale DNA methylation analysis server based on RRBS…

A comprehensive genome-scale DNA methylation analysis server based on RRBS data. RRBS-Analyser can assess sequencing quality, generate detailed statistical information, align the bisulfite-treated…

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