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Read alignment 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 PCR. The bisulfite reads are difficult to map to the reference genome due to the high number of mismatches between the converted Ts and the original Cs.

Source text:
(Lim et al., 2012) BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol.

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Segemehl
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Maps short sequencer reads to reference genomes. Segemehl is a read aligner that allows to detect mismatches, insertions and deletions. The software implements a matching strategy based on enhanced suffix arrays (ESA): it aims to find the best-scoring seed for each suffix of a read. The tool lack, which rescues unmapped RNAseq, reads and works in conjunction with segemehl and many other frequently used split-read aligners, is distributed together with it.
BS Seeker
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Allows to map the bisulfite-treated short reads. BS Seeker is a bisulfite sequencing (BS) alignment tool that performs genome indexing, read alignment and DNA methylation levels calling for each cytosine. The software was improved utilizing multiple short-read mapping aligners, supporting gapped mapping and local alignment and building special indexes for handling reduced represented bisulfite sequencing (RRBS) data.
Bismark
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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 paired-end mapping of both directional and non-directional bisulfite libraries. The output of Bismark is easy to interpret and is intended to be analysed directly by the researcher performing the experiment.
Nanopolish
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 from a directory of FAST5 files; (ii) nanopolish eventalign which aligns signal-level events to k-mers of a reference genome; (iii) nanopolish variants which detects single nucleotide polymorphisms (SNPs) and indels with respect to a reference genome; and (iv) nanopolish variants –consensus which calculates an improved consensus sequence for a draft genome assembly. Furthermore, Nanopolish contains an experimental option that will use event durations to improve the consensus accuracy around homopolymers.
SignalAlign
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 (HMM) software package. With appropriate inputs, characters in the reference sequence can be flagged as ambiguous, meaning multiple bases will be probabilistically aligned to a position. Right now, the program the program supports aligning cytosine variants (5-mC and 5-hmC) and adenine variants (6-mA) to a position.
BatMeth
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 allows asymmetric bisulfite conversion to be detected by labeling the corresponding reference genome with the hit. It integrates novel mismatch counting, list filtering, mismatch stage filtering and fast mapping onto two indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools.
GNUMAP / Genomic Next-generation Universal MAPper
Offers a platform dedicated to map next generation sequencing (NGS) data. GNUMAP combines a Needleman–Wunsch method, statistical mapping algorithms and a full-text index in minute space (FM-index). The application leverages additional information to enhance exploitable data. It is able to determine spike regions in the reference genome as well as to manage repetitive regions. The results can be exported towards the UCSC Genome Browser or Affymetrix’s Integrated Genome Browser for further visualization.
MethylCoder
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 accounts for soft-masked alignments and overlapping paired-end reads. MethylCoder outputs data in text and binary formats in addition to the final alignment in SAM format, so that common high-throughput sequencing tools can be used on the resulting output. It is more flexible than existing software tool and competitive in terms of speed and memory use.
BRAT / Bisulfite-treated Reads Analysis Tool
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 files containing reads and mates of different lengths. BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing programs. The software package includes tools to end-trim low-quality bases of the reads and to report nucleotide counts for mapped reads on the reference genome.
ERNE / Extended Randomized Numerical alignEr
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 reduce memory requirements preserving its speed and accuray. ERNE 2 comprises ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), ERNE-FILTER (quality trimming and contamination filtering), and parallel version of the aligners (ERNE-PMAP and ERNE-PBS5). The alignment core supports indels and one long gap.
BRAT-nova / Bisulfite-treated Reads Analysis Tool-nova
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 supports local alignment by allowing one indel per read. It is very fast and accurate. On the human genome, BRAT-nova is 2-7 times faster than state-of-the-art aligners, while maintaining the same percentage of uniquely mapped reads and space usage. On synthetic reads, BRAT-nova is 2-8 times faster than state-of-the-art aligners while maintaining similar mapping accuracy, methylation call accuracy, methylation level accuracy, and space efficiency.
bicycle / BIsulfite-based methylCYtosine CalLEr
Analyzes whole genome bisulfite sequencing (WGBS) data. bicycle is a next-generation sequencing (NGS) bioinformatic pipeline that can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols and from single-end and paired-end sequencing. It also performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH). It provides statistical methylcytosine calling and offers several filters to screen reads.
SMAP / Streamlined Methylation Analysis Pipeline
Allows to extract multiple types of information (such as DMCs, DMRs, SNPs and ASM) from various types of RRBS and Bis-seq data. SMAP is designed to be an easy-to-use, one-stop and sophisticated package for methylation analyses. The pipeline consists of seven operational stages: (i) reference preparation, (ii) read preparation, (iii) alignment, (iv) calculation of methylation rate, (v) differentially methylated regions (DMR) detection, (vi) single nucleotide polymorphism (SNP) and allele-specific DNA methylation (ASM) calling and (vii) summarization.
TRACE-RRBS / Targeted Alignment and Artificial Cytosine Elimination for RRBS
Maps reduced representation bisulfite sequencing (RRBS) reads and determination of the CpG methylation status of each cytosine locus. TRACE-RRBS aligns sequence reads to a small fraction of the genome where RRBS protocol targets on. This software manages to achieve high correlation of aligned reads with 450k microarray data. Correlation between accuracy of methylation quantification and nearby CpG is enhanced by the end repair artificial cytosine removal.
Methy-Pipe
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 annotation and visualization. Specifically, Methy-Pipe uses Burrow-Wheeler Transform (BWT) algorithm to directly align bisulfite sequencing reads to a reference genome and implements a novel sliding window based approach with statistical methods for the identification of differentially methylated regions (DMRs). The capability of processing data parallelly allows it to outperform a number of other bisulfite alignment software packages.
WBSA / Web Service for Bisulfite Sequencing Data Analysis
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 also allows CHG and CHH analysis. BWA is incorporated as its mapping software. WBSA can be applied to DNA methylation researches for animals and plants and it provides advanced analysis for both WGBS and RRBS. It can also identify differently methylated regions (DMRs) in different strings. WBSA includes six modules: Home, WGBS, RRBS, DMR, Documents and Downloads, and provides the executable package for downloads and local installation. WGBS and RRBS modules include four main steps: pre-processing of reads and reference, alignment to the reference, identification of methylcytosines and annotation. DMR module includes DMRs identification and annotation of the correlative genes.
GPU-BSM
Maps bisulfite-treated reads and estimates methylation levels. GPU-BSM is an accurate application that exploits the 3-letter nucleotide alphabet reduction strategy. It is mainly based on SOAP3-dp, a short-read mapping tool able to take advantage of the computational power of modern Graphics Processing Units (GPU). It supports ungapped and gapped (global and local) alignment with libraries generated with both whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS).
BAM-ABS
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 and real hairpin bisulfite sequencing data show that our method can effectively assign approximately 70% of the multireads to their best locations with up to 90% accuracy, leading to a significant increase in the overall mapping efficiency. Moreover, the assignment model shows robust performance with low coverage depth, making it particularly attractive considering the prohibitive cost of bisulfite sequencing. Additionally, results show that longer reads help improve the performance of the assignment model. The assignment model is also robust to varying degrees of methylation and varying sequencing error rates. Finally, incorporating prior knowledge on mutation rate and context specific methylation level into the assignment model increases inference accuracy. Our scoring method can be used to effectively improve the mapping results of bisulfite sequencing data.
Bwa-meth
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 converted reads directly to the aligner and streaming the alignments directly to a well-formatted alignment file suitable for use in downstream tools. In addition, it works well without quality-trimming, thereby reducing storage requirements 3-fold by not creating quality-trimmed or converted reads.
RRBS-Analyser
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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 short reads to reference genome, identify and annotate the methylcytosines (5mCs) and associate them with different genomic features in CG, CHG, and CHH content. RRBS-Analyser supports detection, annotation, and visualization of differentially methylated regions (DMRs) for multiple samples from nine reference organisms. Moreover, RRBS-Analyser provides researchers with detailed annotation of DMR-containing genes, which will greatly aid subsequent studies. The input of RRBS-Analyser can be raw FASTQ reads, generic SAM format, or self-defined format containing individual 5mC sites. RRBS-Analyser can be widely used by researchers wanting to unravel the complexities of DNA methylome in the epigenetic community.
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