accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Both single and paired ends are supported.
EpiGRAPH enables biologists to analyze genome and epigenome datasets with powerful statistical and machine learning methods. In a typical workflow, the user uploads a set of genomic regions of interest (e.g. experimentally mapped enhancers, hotspots of epigenetic regulation or sites exh...
Omixon Target Standard, Target HLA and Target Pro are designed to help clinical, diagnostic and research labs to efficiently get the maximum accuracy and precision from their targeted NGS data.
CANGS is a flexible and user-friendly utility to trim sequences, filter low quality sequences, and produce input files for further downstream analyses for 454 sequences. CANGS can be used to assign the taxonomic grouping based on similarity with sequences from the NCBI database
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Lasergene is a comprehensive DNA and protein sequence analysis software suite comprised of seven applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design.
标签：Alignment, De novo sequencing,De-novo assembly, Genomics,InDel discovery, Integrated solution, Mapping,Phylogenetics, Protein structure analysis, Read alignment, SNP discovery,Sequence analysis,Transcription Factor Binding Site identification
TagCleaner can be used to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets. TagCleaner is available as both standalone and web-based versions.
GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.
We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content.
Pipeline for fast, simple processing of BiSulfite-treated reads into methylation data. Includes scripts for analysis and visualization. In addition to a binary output, the direct output of methylcoder is a text file that indicates per-nucleotide methylation context (CG/CHG/CHH) and meth...
标签：Genomics, Sequencing, DNA methylation, Epigenomics
BiQ Analyzer HT is an enhanced version of BiQ Analyzer that provides extensive support for high-throughput bisulfite sequencing. BiQ Analyzer HT facilitates the processing, quality control and initial analysis of single-basepair resolution DNA methylation data. It was developed for deep...
标签：Epigenomics, DNA methylation,Bisulfite Sequencing
DeconSeq can be used to automatically detect and efficiently remove any type of sequence contamination from metagenomic datasets, including human or other host sequences. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read lengt...
Pash 3.0 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 sequencing
V-Xtractor uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences.