• GATK

  • Referenced in 15 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...
  • SHRiMP

  • Referenced in 15 articles [sw17146]
  • color-space reads. The development of Next Generation Sequencing technologies, capable of sequencing hundreds...
  • BEDTools

  • Referenced in 12 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...
  • CMA-ES

  • Referenced in 105 articles [sw05063]
  • some individuals are selected for the next generation based on their fitness or objective function ... Like this, over the generation sequence, individuals with better and better f-values are generated...
  • 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...
  • CloudBurst

  • Referenced in 7 articles [sw12025]
  • read mapping with MapReduce. Motivation: Next-generation DNA sequencing machines are generating an enormous amount ... sequence data, placing unprecedented demands on traditional single-processor read-mapping algorithms. CloudBurst ... read-mapping algorithm optimized for mapping next-generation sequence data to the human genome...
  • 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...
  • BS Seeker

  • Referenced in 6 articles [sw23481]
  • bisulfite sequencing. BACKGROUND: Bisulfite sequencing using next generation sequencers yields genome-wide measurements...
  • VarScan

  • Referenced in 7 articles [sw27471]
  • detects variants (SNPs and indels) in next-generation sequencing data. The new release (VarScan...
  • ZOOM

  • Referenced in 7 articles [sw31864]
  • Zillions of oligos mapped. Motivation: The next generation sequencing technologies are generating billions of short...
  • 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...
  • BSMAP

  • Referenced in 5 articles [sw23515]
  • genome bisulfite sequence MAPping program. BACKGROUND: Bisulfite sequencing is a powerful technique to study ... unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect...
  • featureCounts

  • Referenced in 5 articles [sw17317]
  • general-purpose read summarization program. Motivation: Next-generation sequencing technologies generate millions of short sequence...
  • Segmentor3IsBack

  • Referenced in 5 articles [sw21077]
  • experiments requiring biological expertise. The expanding Next Generation Sequencing technologies and their enhanced precision allow...
  • 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...
  • Trimmomatic

  • Referenced in 4 articles [sw17091]
  • Illumina sequence data. Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed...