BFAST : An alignment tool for fast and accurate mapping of short reads to reference sequences
BWA : A software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
Bowtie : An ultrafast, memory-efficient short read aligner.
Novoalign/NovoalignCS : An aligner for single-ended and paired-end reads from the Illumina Genome Analyser.
MAQ : Mapping and Assembly with Quality, builds assembly by mapping short reads to reference sequences.
SHRiMP : A software package for aligning genomic reads against a target genome.
SOAP2 : (Short Oligonucleotide Analysis Package), a program for faster and efficient alignment for short oligonucleotide onto reference sequences.
SSAHA2 :(Sequence Search and Alignment by Hashing Algorithm), a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.
GASSST : A Global Alignment Short Sequence Search Tool .
PASS : A program to align short sequences .
MicroRazerS : A rapid alignment of small RNA reads. .
SeqMap : A tool for mapping large amount of oligonucleotide to the genome .
PerM : An Efficient mapping of short sequences accomplished with periodic full sensitive spaced seeds .
GAMES : Identifies and annotates mutations in next-generation sequencing projects.
CoNAn-SNV : A probabilistic framework for the discovery of single nucleotide variants in WGSS data.
LoFreq : A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.
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.
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.
MoDIL : Detecting INDEL Variation with Clone-end Sequencing - Resources and Source Code .
PyroHMMvar : A program to call short indels and SNPs for Ion Torrent and 454 data.
svseq2 : An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.
BreakDancer: A tool for detecting five types of SVs (insertions, deletions, inversions, inter- and intra-chromosomal translocations) from next generation paired-end sequencing reads.
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.
destruct: A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.
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.
GENSENG : A software detecting CNVs from NGS data.
CNV-seq : A method for detecting DNA copy number variation (CNV) using high-throughput sequencing .
mrCaNaVaR : A copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions.
ANNOVAR: An efficient software tool to use update-to-date information to functionally annotate genetic variants detected from diverse genomes.
PolyPhen-2: (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.
CHASM: (Cancer-specific High-throughput Annotation of Somatic Mutations) is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells.
SIFT: predicts whether an amino acid substitution affects protein function.
ALLPATHS-LG : High quality genome assembly from low cost data.
Celera Assembler : A de novo whole-genome shotgun (WGS) DNA sequence assembler.
Geneious : Software for analyzing both your high-throughput and Sanger sequencing data .
LOCAS : A software to assemble short reads of next generation sequencing technologies at low coverage.
Contrail : A Hadoop based genome assembler for assembling large genomes in the clouds.
MIRA : A whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). .
Velvet : a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom .
CongrPE : a de novo assembly algorithm, named CongrPE, for Next-Generation Sequencing technology.
ZORRO : A hybrid sequencing technology assembler.
ABySS : Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler .
wANNOVAR : Annotating genetic variants for personal genomes via the web.
ANNOVAR : An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others).
SVA : (Sequence Variant Analyzer) Software to annotate,visualize and analyze the genetic variants identified through NGS.
WebApollo : Browser based tool for visualization and editing of sequence annotations .
Chaos : A Perl-based system for annotation of variants identified in high-throughput sequencing experiments developed at the Wellcome Trust Centre for Human Genetics (WTCHG).