• GATK

  • Referenced in 11 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...
  • CloudBurst

  • Referenced in 7 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...
  • CNV-seq

  • Referenced in 9 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 9 articles [sw13528]
  • rapidly changing field of next-generation sequencing. The main results of GAGE have now been...
  • FindPeaks

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

  • Referenced in 7 articles [sw17158]
  • analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics...
  • SNVMix

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

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

  • Referenced in 6 articles [sw27471]
  • detects variants (SNPs and indels) in next-generation sequencing data. The new release (VarScan...
  • featureCounts

  • Referenced in 5 articles [sw17317]
  • general-purpose read summarization program. Motivation: Next-generation sequencing technologies generate millions of short sequence...
  • 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...
  • GRASS

  • Referenced in 4 articles [sw12609]
  • GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Motivation: The increasing availability...
  • RazerS

  • Referenced in 4 articles [sw22766]
  • mapping. MOTIVATION: During the past years, next-generation sequencing has become a key technology...
  • BM-map

  • Referenced in 2 articles [sw10924]
  • Bayesian mapping of multireads for next-generation sequencing data. Next-generation sequencing (NGS) technology generates...
  • miRanalyzer

  • Referenced in 2 articles [sw29579]
  • microRNA detection and analysis tool for next-generation sequencing experiments. Next-generation sequencing allows...
  • HIVE-hexagon

  • Referenced in 2 articles [sw23018]
  • high-performance, parallelized sequence alignment for next-generation sequencing data analysis. Due to the size ... Next-Generation Sequencing data, the computational challenge of sequence alignment has been vast. Inexact alignments...
  • Bambino

  • Referenced in 2 articles [sw17426]
  • variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Summary ... detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which...
  • PurityEst

  • Referenced in 2 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...