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
1. SAMtools
Various utilities for processing alignments in the SAM format, including variant calling and alignment viewing. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. ...
标签:SNP discovery
2. Maq
Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data. Maq stands for Mapping and Assembly with Quality. It builds assembly by mapping short reads to reference ...
标签:Genomics, SNP discovery
3. SOAP
SOAP (Short Oligonucleotide Alignment Program) is a program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. SOAP2 is an updated program based on Burrows-Wheeler Transform. has been in evolution from a single alignment tool to a tool pac...
标签:SNP discovery
4. GATK
The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorit...
标签:SNP discovery
5. MIRA
MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler Whole Genome Shotgun and EST sequence assembler
标签:De-novo assembly, SNP discovery, RNA-Seq Alignment
6. SOAPsnp
SOAPsnp is an accurate consensus sequence builder based on soap1 and SOAPaligner/soap2's alignment output. It calculates a quality score for each consensus base, which can be used for any latter process to call SNPs.
标签:SNP discovery
7. Shore
Analysis suite for short read data.
标签:Structural variation, SNP discovery
8. VarScan
VarScan, an open source tool for variant detection that is compatible with several short read align-ers.
标签:SNP discovery
9. ERGO Genome Analysis and Discovery System
ERGO provides a systems-biology informatics toolkit centered on comparative genomics to capture, query and visualize sequenced genomes. Building upon the most comprehensive genomic database available anywhere integrated with the largest collection of microbial metabolic and non-metaboli...
标签:Metabolic reconstruction,Phylogenetics, Comparative genomics, SNP Annotation, SNP discovery, Alignment, Exome analysis, Metagenomics,Pathway analysis, Comparative transcriptomics, Functional Genomics, Gene Expression Analysis, Genome Wide Association Stud
10. CLCbio Genomics Workbench
De novo and reference assembly SNP and small indel detection and annotation.
标签:Genomics, Whole Genome Resequencing, De-novo assembly, SNP discovery, InDel discovery, ChIP-Seq, RNA-Seq,MiRNA, Transcriptomics
11. SeqMan NGen
Sequence assembly software using traditional, next-gen, and third-gen techonologies. Subsequent analysis of the assembly, including SNP discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene.
标签:Genomics, De-novo assembly, De novo transcriptome assembly,Whole Genome Resequencing, SNP discovery, InDel discovery,ChIP-Seq, RNA-Seq Alignment
12. Syzygy
Software to identify variants from pooled sequencing data
标签:SNP discovery, InDel discovery
13. PyroBayes
PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines.
标签:SNP discovery
14. Crossbow
Crossbow is a cloud-computing software tool that combines the aligner BOWTIE and the SNP caller SOAPsnp. Crossbow is a cloud-computing software tool that combines the aligner BOWTIE and the SNP caller SOAPsnp.
标签:SNP discovery
15. SNPSeeker
Identification of SNPs in pooled genomic samples
标签:SNP discovery
16. Trans-ABySS
Trans-ABySS is a software package that is designed to analyze ABySS-assembled whole-genome shotgun transcriptome data.
标签:RNA-Seq, SNP discovery, Fusion genes, InDel discovery, Fusion transcripts
17. CloudBurst
CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes.
标签:SNP discovery, Genotyping,Personal genomics
18. SNVMix
Detects single nucleotide variants from next generation sequencing data.
标签:SNP discovery
19. Atlas-SNP2
Atlas-SNP2 is a SNP discovery tool developed for next generation sequencing platforms
标签:SNP discovery
20. SNIP-Seq
Tool for discovering SNPs in population sequencing data
标签:SNP discovery