标签云

Alignment Allele-specific transcription Alternative Splicing Barcoding Bisulfite Sequencing Cancer biology ChIP-exo ChIP-on-chip ChIP-Seq Clone verification Comparative genomics Comparative transcriptomics Comparison Conversion Copy number estimation De novo assembly De novo sequencing De-novo assembly DNA methylation DNA-Seq Epigenomics Evaluation and validation Exome and whole genome variant detection Framework Functional Genomics Gene expression Gene regulatory network analysis General bioinformatics (pipeline) Genomic Assembly Genomic Assembly Evaluation Genomic Assembly Validation Genomics Identification InDel discovery Infrastructure Mapping Mass Accuracy Metagenomics Metatranscriptomics Next Generation Sequencing Nucleic acid sequence analysis Nucleic acid structure comparison Pairwise structure alignment Peptide identification (DB) Peptide identification (De novo) Peptide identification (lib match) Personal genomics Phylogenetics Population genetics Population Genomics Protein Inference Quality Control Quantitation Raw Data Raw Data / Conversion Read alignment Reference assembly Regulatory genomics Regulatory genomics epigenomics Resequencing Results processing RNA structure prediction RNA-Seq RNA-Seq Alignment RNA-Seq Quantitation Search and retrieval Sequence analysis Sequence database search Sequence functional annotation Sequence motif discovery Sequence motif recognition Sequence Quality Control Sequencing Small RNA transcriptome SNP Annotation SNP discovery SNPs Somatic mutations Structural variation Targeted assembly Targeted resequencing Transcription Factor Binding Site identification Transcriptome Viral genomics Whole gene prediction Whole Genome Resequencing Whole Genome Resequencing Analysis  Alignment  Alternative Splicing  Bisulfite Sequencing  ChIP-on-chip  ChIP-Seq  De novo assembly  De novo transcriptome assembly  De-novo assembly  DNA methylation  DNA-Seq  Exome and Whole genome variant detection  Fusion finding  Fusion genes  Fusion transcripts  Genomic Assembly  Genomics  Genotyping  High-throughput sequencing  In vitro selection  InDel discovery  Mapping  Metagenomics  MiRNA  MiRNA-Seq  Motif analysis  Next Generation Sequencing  Personal genomics  Phylogenetics  Population genetics  Population genomics  Read alignment  Reference assembly  Regulatory genomics  RNA Seq analysis  RNA-Seq  RNA-Seq Quantitation  Sequence analysis  Sequence annotation  Sequencing  Small RNA transcriptome  SNP discovery  Structural variation  Targeted resequencing  Transcription Factor Binding Site identification  Transcriptomics  Whole Genome Resequencing  Whole Genome Resequencing Analysis 基因组注释 基因预测 多重序列比对 多重比对 序列拼接 推荐 比较基因组 重复序列
161. NextGENe
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
162. Ngs-pipeline
Complete solution for human re-sequencing projects
标签:Personal genomics,Epigenomics, Structural variation
163. Ngs.plot
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...
标签:Epigenomics, Transcriptomics
164. NGSView
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 ...
标签:Genomics
165. PeakAnalyzer
PeakAnalyzer is a set of applications for processing ChIP signal peaks.
标签:Functional Genomics
166. PoPoolation2
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...
标签:Population genetics, Genomics
167. RAST
"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."
标签:Genomics, Phylogenetics
168. RTG Investigator
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
169. SCALCE
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.
标签:Genomics
170. SeqPrep
Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.
标签:Genomics, De-novo assembly
171. SequenceVariantAnalyzer
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, ...
标签:Personal genomics, Genomics,Sequence analysis
172. Sherman
bisulfite-treated Read FastQ Simulator
标签:Genomics, Bisulfite Sequencing, DNA methylation
173. Sibelia
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...
标签:Genomics
174. SplicingViewer
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.
标签:RNA-Seq, Genomics
175. Syapse
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
176. Vcflib
API and command line utilities for the manipulation of VCF files.
标签:Genomics
177. VirusSeq
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...
标签:Viral genomics
178. WebApollo
WebApollo is a browser-based tool for distributed community annotation of sequences.
标签:Genomics, Sequence annotation,Sequence functional annotation
179. ZORRO
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.
标签:Genomic Assembly, Genomics