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
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
GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Man...
FusionAnalyser is a new graphical, event-driven tool dedicated to the identification of driver fusion rearrangements in human cancer through the analysis of paired-end high-throughput transcriptome sequencing data. Tested on Illumina. Requires short, paired-end sequences.
BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically esti...
标签：SNP discovery, Genotyping, DNA methylation, Bisulfite Sequencing
featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge...
The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools ...
标签：Epigenomics, DNA methylation,Bisulfite Sequencing
RUbioSeq has been developed to facilitate the primary and secondary analysis of resequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (SNVs and CNVs) and to perform Bisulfite-seq analyses automatically. RUbioSeq's variant anal...
标签：Exome analysis, Copy number estimation, Bisulfite Sequencing
A free genome browser for exploring sequencing pile-up and coverage data with numerous annotation tracks hosted on the cloud.
标签：Sequence analysis, DNA-Seq,Alignment, De novo sequencing,Exome analysis, Exome and whole genome variant detection, Genetics, Whole Genome Resequencing, Next Generation Sequencing,Genomics
Copy number analysis for exome-sequencing / targeted-resequencing. Two methods of analysis available: Case vs Control, or Case vs Baseline. Function available for creating a baseline from multiple samples.
标签：Next Generation Sequencing,Cancer biology, Genomics, Copy number estimation
Skewer implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences.
标签：Small RNA Sequencing, RNA-Seq,Whole Genome Resequencing, De novo Sequencing
Rsubread is Bioconductor R package, which provides facilities to performing read alignments using the Subread aligner. It also includes other functionalities such as featureCounts read summarization function.
The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-e...
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2.
标签：Epigenomics, Bisulfite Sequencing, DNA methylation