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  • GATK
  • Referenced in 17 articles [sw12019]
  • MapReduce framework for analyzing next-generation DNA sequencing data. Next-generation DNA sequencing (NGS) projects ... among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone ... robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce...

  • BEDTools
  • Referenced in 11 articles [sw17302]
  • format. BEDTools also supports the comparison of sequence alignments in BAM format to both ... user to compare large datasets (e.g. next-generation sequencing data) with both public and custom...

  • CNV-seq
  • Referenced in 11 articles [sw17970]
  • detect copy number variation using shotgun sequencing, CNV-seq. The method is based ... resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount...

  • GAGE
  • Referenced in 11 articles [sw13528]
  • rapidly changing field of next-generation sequencing. The main results of GAGE have now been...

  • RAST
  • Referenced in 8 articles [sw17158]
  • analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics...

  • FindPeaks
  • Referenced in 7 articles [sw29575]
  • parallel short-read sequencing technology. Summary: Next-generation sequencing can provide insight into protein...

  • VarScan
  • Referenced in 8 articles [sw27471]
  • detects variants (SNPs and indels) in next-generation sequencing data. The new release (VarScan...

  • CloudBurst
  • Referenced in 6 articles [sw12025]
  • Motivation: Next-generation DNA sequencing machines are generating an enormous amount of sequence data, placing ... read-mapping algorithm optimized for mapping next-generation sequence data to the human genome...

  • SNVMix
  • Referenced in 4 articles [sw29569]
  • SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Motivation: Next-generation sequencing...

  • Trimmomatic
  • Referenced in 6 articles [sw17091]
  • Illumina sequence data. Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed...

  • seqCBS
  • Referenced in 6 articles [sw12152]
  • Copy Number Profiling using Next-Generation Sequencing. It has new model and test statistics based...

  • featureCounts
  • Referenced in 6 articles [sw17317]
  • general-purpose read summarization program. Motivation: Next-generation sequencing technologies generate millions of short sequence...

  • GRASS
  • Referenced in 5 articles [sw12609]
  • GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Motivation: The increasing availability...

  • RAPSearch2
  • Referenced in 3 articles [sw23045]
  • efficient protein similarity search tool for next-generation sequencing data. SUMMARY: With the wide application ... next-generation sequencing (NGS) techniques, fast tools for protein similarity search that scale well...

  • SNVer
  • Referenced in 3 articles [sw36884]
  • analysis of pooled or individual next-generation sequencing data. We develop a statistical tool SNVer ... analysis of pooled or individual next-generation sequencing (NGS) data. We formulate variant calling...

  • PurityEst
  • Referenced in 3 articles [sw24696]
  • purity of human tumor samples using next-generation sequencing data. We developed a novel algorithm ... with a matched normal tissue using next-generation sequencing data. We applied our tool...

  • Readjoiner
  • Referenced in 4 articles [sw37848]
  • Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation...

  • PerM
  • Referenced in 4 articles [sw35278]
  • spaced seeds . Motivation: The explosion of next-generation sequencing data has spawned the design...

  • MetaSim
  • Referenced in 4 articles [sw23453]
  • MetaSim - A Sequencing Simulator for Genomics and Metagenomics. Background: The new research field of metagenomics ... into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase...

  • FragGeneScan
  • Referenced in 4 articles [sw17159]
  • error-prone reads. The advances of next-generation sequencing technology have facilitated metagenomics research that...