Assists users with DNA sequence analysis. Sequencher is a graphical application that integrates the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. It can generate unique data visualizations using customized plots and graphs that produces ready-to-print graphs. This model also includes an extensive Sanger analysis features.
Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. methylKit is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.
Provides a toolbox for genomic analyses on BAM files. BamBam is a package of more than 10 applications intending to assist users in usual tasks including phylogeny inference or differential expression analysis. It includes features to: (i) quantify reads mapped to each gene in a genome; (ii) detect single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) or (iii) summarize read coverage of sequences or regions.
A comprehensive tool for identification and analysis of the methylation patterns of genomic regions from bisulfite sequencing data. CpG_MPs first normalizes bisulfite sequencing reads into methylation level of CpGs. Then it identifies unmethylated and methylated regions using the methylation status of neighboring CpGs by hotspot extension algorithm without knowledge of pre-defined regions. Furthermore, the conservatively and differentially methylated regions across paired or multiple samples (cells or tissues) are identified by combining a combinatorial algorithm with Shannon entropy.
An efficient, specialized and highly automated mapping and annotation tool for RNA bisulfite sequencing data. Focusing on both CG and non-CG methylation, BS-RNA can handle the mapping and annotation of either single- or paired-end sequencing reads of directional bisulfite libraries. This tool provide more comprehensive annotation information such as the distribution of cytosine methylation in both gene and transcript levels.
A fragment-based approach for investigating DNA methylation patterns for reduced representation bisulphite sequencing data. DMAP can directly import the output from any bisulphite aligner in sequence alignment/map (SAM) format and identify differential methylation.