• GATK

• Referenced in 16 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...

• 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...

• VarScan

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

• 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...

• Trimmomatic

• Referenced in 5 articles [sw17091]
• Illumina sequence data. Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed...

• GRASS

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

• featureCounts

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

• 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...

• 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...

• FragGeneScan

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

• 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...