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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...
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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...
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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...
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GAGE
- Referenced in 11 articles
[sw13528]
- rapidly changing field of next-generation sequencing. The main results of GAGE have now been...
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RAST
- Referenced in 8 articles
[sw17158]
- analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics...
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FindPeaks
- Referenced in 7 articles
[sw29575]
- parallel short-read sequencing technology. Summary: Next-generation sequencing can provide insight into protein...
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VarScan
- Referenced in 8 articles
[sw27471]
- detects variants (SNPs and indels) in next-generation sequencing data. The new release (VarScan...
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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...
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SNVMix
- Referenced in 4 articles
[sw29569]
- SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Motivation: Next-generation sequencing...
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Trimmomatic
- Referenced in 6 articles
[sw17091]
- Illumina sequence data. Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed...
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seqCBS
- Referenced in 6 articles
[sw12152]
- Copy Number Profiling using Next-Generation Sequencing. It has new model and test statistics based...
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featureCounts
- Referenced in 6 articles
[sw17317]
- general-purpose read summarization program. Motivation: Next-generation sequencing technologies generate millions of short sequence...
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GRASS
- Referenced in 5 articles
[sw12609]
- GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Motivation: The increasing availability...
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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...
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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...
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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...
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Readjoiner
- Referenced in 4 articles
[sw37848]
- Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation...
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PerM
- Referenced in 4 articles
[sw35278]
- spaced seeds . Motivation: The explosion of next-generation sequencing data has spawned the design...
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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...
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FragGeneScan
- Referenced in 4 articles
[sw17159]
- error-prone reads. The advances of next-generation sequencing technology have facilitated metagenomics research that...