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  •  InDel discovery
1. BreakDancer
BreakDancer is an application for detecting structural rearrangements and indels in short read sequencing data BreakDancer, released under GPLv3, is a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It include...
标签：Genomics, Structural variation, InDel discovery
2. 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
3. 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
4. Syzygy
Software to identify variants from pooled sequencing data
标签：SNP discovery, InDel discovery
5. 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
6. MoDIL
Program to detect small indels in next generation sequencing data
标签：Genomics, InDel discovery
7. NovelSeq
A computational framework to discover the content and location of long novel sequence insertions using paired-end sequencing data
标签：Structural variation, InDel discovery
8. VAAL
VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants.
标签：Structural variation, SNP discovery, InDel discovery
9. Omixon Variant Toolkit
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.
标签：Comparative genomics, Mapping,Sequence analysis, Read alignment, InDel discovery,SNP discovery
10. SRMA
SRMA is a short read micro re-aligner for next-generation high throughput sequencing data.
标签：SNP discovery, InDel discovery
11. Atlas Suite
Atlas is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequecing (WECS) data. SNPs may be called using the Atlas-SNP2 application and indels may be called usin...
标签：SNP discovery, InDel discovery
12. ECHO
Reference-free short read error correction from diploid genomes, with explicit modeling of heterozygous sites.
标签：SNP discovery, InDel discovery
13. VARiD
VARiD is a variation detection framework for both color-space and letter-space platforms
标签：Genomics, SNP discovery, InDel discovery
14. Breakpointer
Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structur...
标签：Exome and Whole genome variant detection, InDel discovery
15. Illuminator
Software for machines running Windows to identify variants in Illumina short read data.
标签：SNP discovery, InDel discovery
16. Kissnp
kisSnp compares two sets of NGS raw reads, detecting Single Nucleotide Polymorphism occurring between the two sets. The two sets typically come from the sequencing of two individuals from the same species or from closely related species.
标签：Comparative genomics,Comparative transcriptomics,Gene annotation retrieval, SNP discovery, InDel discovery
17. Array Suite (Array Studio/Server)
Array Studio is a complete analysis and visualization package for NextGen sequencing data, as well as other -OMIC data types. Array Server is a backend enterprise server for storage and analysis of -OMIC and NextGen sequencing data.
标签：Genomics, SNP discovery, InDel discovery
18. Breakway
Breakway is a suite of programs that take aligned genomic data and report structural variation breakpoints.
标签：Whole Genome Resequencing,Genomics, Structural variation, InDel discovery
19. 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
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