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.
Executes alignments for single- and paired-end reads. GSNAP exploits probabilistic models or a database of known splice sites to identifies short and long-distance splicing in individual reads. This software uses a constrained search strategy for producing candidate genomic regions by combining position lists from oligomers across the entire read. The search procedure works at the oligomer level, which differs from the nucleotide-level backtracking procedures.
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.
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.
Aims to perform both ungapped and gapped alignment. SOAP is a program including special modules for alignment of pair-end, small RNA and messenger RNA (mRNA) tag sequences. It allows either a certain number of mismatches or one continuous gap for aligning a read onto the reference sequence.
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 mapping approaches, BSMAP is faster, more sensitive and more flexible.
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.
Identifies DNA modifications in the case where 5-mC can be distinguished from cytosine by careful analysis of the electrical current signals. Nanopolish computes the log-likelihood ratio between an unmethylated version of a reference genome substring and a version that contained at least one ‘CG’ dinucleotide. It employs a signal-level hidden Markov model (HMM) method to work. This tool can increase the consensus accuracy around homopolymers.