de novo and reference assembly of Roche/454, Illumina and SOLiD data. Uses a novel Condensation Assembly Tool approach where reads are joined via "anchors" into mini-contigs before assembly which reduces sequencing errors. Requires Win or MacOS.
标签：De novo sequencing,Metagenomics, SNP discovery,InDel discovery, Targeted resequencing
ngs.plot is a program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions. The signature advantage of ngs.plot is that it collects a large database of functional elements for many genomes. A user can ask for a functionally impo...
High-throughput sequencing technologies introduce novel demands on tools available for data analysis. We have developed NGSView, a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions ...
PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, f...
"RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating complete or nearly complete bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree."
Comprehensive analysis pipelines powered with unique mapping speed and sensitivity deliver deep genomic analysis in variant detection and metagenomic applications with Illumina, Ion Torrent, Complete Genomics and Roche 454 data sets.
标签：Exome and whole genome variant detection, Metagenomics, SNP discovery, InDel discovery
SCALCE (skeɪlz) is fast FASTQ compression utility that utilizes locally consistent parsing for better compression rate. It achieves around 2X more compression than gzip alone.
DNA sequence information underpins genetic research, enabling discoversies of important biological or medical benefit. Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of linkage disequilibrium, thus, in theory, ...
Sibelia: A comparative genomic tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studi...
SplicingViewer is an integrated tool developed to enable users to detect the splice junctions, annotate alternative splicing events, and visualization of the patterns of alternative splicing events.
Syapse is a platform and application suite for bringing together omics and clinical data.
标签：Allele-specific transcription,DNA methylation, DNA-Seq,InDel discovery, SNP discovery, Structural variation, RNA-Seq, Small RNA transcriptome, ChIP-Seq,Comparative genomics,Comparative transcriptomics,Epigenomics, Genomics,Personal genomics, Population ge
We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on RNA-Seq data of 256 TCGA human cancer samples. Using these data, we showed that VirusSeq accuratel...
ZORRO is an hybrid sequencing technology assembler. It takes to sets of pre-assembled contigs and merge them into a more contiguous and consistent assembly. The main caracteristic of Zorro is the treatment before and after assembly to avoid errors.