******************************************【Mapping】*****************************************    

BFAST: A fast and accurate tool for mapping of short reads to reference sequences.

BWA: A fast light-weighted tool that aligns short nucleotide sequences to a sequence database.

Bowtie: An ultrafast, memory-efficient short read aligner.

ELAND: A very fast alignment algorithms from Illumina company.

MAQ: A software that builds mapping assemblies from short reads generated by the next-generation sequencing machines.

SHRiMP: A software package for aligning genomic reads against a target genome.

SOAP: A tool package that provides full solution to next generation sequencing data analysis (including a alignment tool SOAPaligner/soap2 etc).

SOLiD bioscope: A software package that is designed specifically to optimize the accuracy of the ABI SOLiD colorspace data.

SWIFT: A software collection for fast index-based sequence comparison.

TopHat: A spliced read mapper for RNA-Seq.

**********************************************【SNV detection】*******************************************

CASAVA: The internal assembler and variant caller Illumina company utilized.

GATK: A multiple-sample, technology-aware SNV and indel caller.

JointSNVMix: A probabilistic model for detection of somatic mutations in normal/tumour pair.

SAMtools: A set of utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer.

SNVMix: A tool for SNV calling based on probabilistic binomial mixture model.

SOAPsnp: A tool for identifying SNVs by Beijing Genomics Institute (BGI).

Strelka: A tool for somatic small-variant calling from sequenced tumor-normal sample pairs.

SomaticSniper: A program to identify SNVs that are different between tumor and normal sample.

VarScan: A platform-independent, technology-independent software tool for identifying SNVs, indels, and CNVs in massively parallel sequencing of individual and pooled samples.

***********************************************【Indel Detection】*****************************************

Dindel: A program for calling small indels from short-read sequence data from Illumina platform.

Pindel: A tool for identifying indels and structural variants at single-based resolution from next-generation sequence data.

SplazerS: A tool for detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing.

******************************************【Structure Variation Detection】******************************

BreakDancer: A tool for detecting five types of SVs (insertions, deletions, inversions, inter- and intra-chromosomal translocations) from next generation paired-end sequencing reads.

CREST: A software that uses the soft-clipped reads to directly map the breakpoints of SVs.

GASV: A tool for identifying and comparing structural variants by computing intersections of breakpoint regions.

HYDRA: A tool for detecting structural variants in both unique and duplicated genomic regions.

PEMer: A software package for detecting SVs from paired-end reads.

R453Plus1Toolbox: An R/Bioconductor package for the analysis of Roche 454 sequencing data.

SVMerge: A tool for SVs analysis by integrating calls from several existing SV callers.

SVDetect: A tool for identifying structural variations from paired-end/mate pair data.

VariationHunter: An tool for identifying structural variations from paired-end WGS data.

*************************************【Copy Number Variation Detection】******************************

CBS: An R package for detecting CNVs using sequencing data.

CMDS: A population-based method for recurrent CNVs analysis from multiple samples.

CNAseg: A tool for Identifying CNVs in cancer from NGS data.

cnvHMM: A tool for CNVs analysis using Hidden Markov algorithm.

CNVnator: A tool for CNV discovery and genotyping from depth of read mapping.

FREEC: A tool for control-free CNVs detection using deep-sequencing data.

RDXplorer: A tool for CNVs detection in whole human genome sequence data using read depth coverage.

SegSeq: A tool for detecting CNVs from short sequence reads.

VarScan: A platform-independent, technology-independent software tool for identifying SNVs, indels, and CNVs in massively parallel sequencing of individual and pooled samples.

************************************************【Annotation】********************************************

ANNOVAR: An efficient software tool to use update-to-date information to functionally annotate genetic variants detected from diverse genomes.

BreakSeq: A pipeline for annotation, classification and analysis of SVs at single nucleotide resolution.

Seattle Seq: An server that provides annotation of SNVs.

*******************************************【Data Visualization】*************************************

Avadis: A software for visualizing and analyzing RNA-Seq data.

CIRCOS: A software package for visualizing genomic events.

IGV: A high-performance visualization tool for interactive exploration of next-generation sequencing data.

Pairoscope: A software package for generating diagrams indicating the relationship of paired end sequencing reads, is most useful for visualizing translocations.

UCSC Genome Browser: A genome browser that provide precise access to sequence and annotation data for any genomic region of specific interest.

****************************************【Fusion Gene Detection】***********************************

BreakFusion: A tool to identify gene fusions from paired-end RNA-Seq data.

Chimerascan: A software for detecting gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.

Comrad: A tool to identify aberrant transcripts and associated rearrangements using low coverage genome data.

defuse: A software for discovering gene fusion from RNA-Seq data.

FusionAnalyser: A software for detecting gene fusions from paired-end RNA-Seq data.

FusionHunter: A tool to identify fusion transcripts from transcriptional analysis of paired-end RNA-seq.

FusionMap: A software to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies.

FusionSeq: A tool to identify fusion transcripts from paired-end RNA-sequencing.

nFuse: A tool for detecting fusion transcripts and associated complex genomic rearrangements from matched RNA-seq and whole genome shotgun sequencing.

SnowShoes-FTD: A tool to find fusions from RNA-Seq data.

ShortFuse: A software to identify fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.

TopHat-Fusion: A software with the ability to align reads across fusion points.

Trans-ABySS: A software to analyses ABySS-assembled contigs from shotgun transcriptome data.

******************************************************THAT'S ALL******************************************