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Read mapping software tools | Bisulfite sequencing data analysis

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…
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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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SignalAlign
Desktop

SignalAlign

Aligns the ionic current signal from the Oxford Nanopore Technologies (ONT)…

Aligns the ionic current signal from the Oxford Nanopore Technologies (ONT) MinION to a reference sequence and inferring properties of the reference sequence. SignalAlign is a hidden Markov model…

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Nanopolish
Desktop

Nanopolish

Provides a nanopore consensus algorithm using a signal-level hidden Markov…

Provides a nanopore consensus algorithm using a signal-level hidden Markov model (HMM). The main subprograms of Nanopolish are: (i) nanopolish extract which extracts reads in FASTA or FASTQ format…

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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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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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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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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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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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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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HPG-Methyl
Desktop

HPG-Methyl

Maps and determines the methylation state of bisulphite reads. HPG-Methyl is a…

Maps and determines the methylation state of bisulphite reads. HPG-Methyl is a Next-Generation Sequencing (NGS) read mapper and methylation context extractor. The strategy used by this software…

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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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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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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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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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Segemehl
Desktop

Segemehl

A software tool to map short sequencer reads to reference genomes. Unlike other…

A software tool to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not…

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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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