Selected NGS Freeware Tool List
Read Mapping Softwares
  • 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.

Structural 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.

  • 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.

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