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References from Challenges in the Setup of Large-scale Next-Generation Sequencing Analysis Workflows. Local targets link to admitted publications; unresolved targets remain external evidence.
CoNCoS: copy number estimation in cancer with controlled support
10.1142/s0219720015500274 · 2015 · External reference
BigBWA: approaching the burrows–wheeler aligner to big data technologies
10.1093/bioinformatics/btv506 · 2015 · External reference
Differential peak calling of ChIP-seq signals with replicates with THOR
2016 · External reference
10.1101/gr.133744.111
10.1101/gr.133744.111 · External reference
ExScalibur: a high-performance cloud-enabled suite for whole exome germline and somatic mutation identification
10.1371/journal.pone.0135800 · 2015 · External reference
10.1038/nmeth.1276
10.1038/nmeth.1276 · External reference
10.1002/humu.23275
10.1002/humu.23275 · External reference
PaPrBaG: a machine learning approach for the detection of novel pathogens from NGS data
10.1038/srep39194 · 2017 · External reference
10.1093/bib/bbs046
10.1093/bib/bbs046 · External reference
10.1093/bioinformatics/bts635
10.1093/bioinformatics/bts635 · External reference
10.1038/nmeth.3407
10.1038/nmeth.3407 · External reference
10.1101/gr.4086505
10.1101/gr.4086505 · External reference
10.1126/science.286.5439.531
10.1126/science.286.5439.531 · External reference
10.1126/science.1229566
10.1126/science.1229566 · External reference
10.1186/1471-2164-12-507
10.1186/1471-2164-12-507 · External reference
Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics
10.1186/s13059-014-0577-x · 2015 · External reference
BarraCUDA - a fast short read sequence aligner using graphics processing units
10.1186/1756-0500-5-27 · 2012 · External reference
Detecting and annotating genetic variations using the HugeSeq pipeline
10.1038/nbt.2134 · 2012 · External reference
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
10.1186/gb-2009-10-3-r25 · 2009 · External reference
10.1093/bioinformatics/btp324
10.1093/bioinformatics/btp324 · External reference
10.1093/bioinformatics/btp352
10.1093/bioinformatics/btp352 · External reference
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
10.1093/bioinformatics/bts276 · 2012 · External reference
10.1186/s13059-014-0550-8
10.1186/s13059-014-0550-8 · External reference
SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner
10.1371/journal.pone.0065632 · 2013 · External reference
Deep neural nets as a method for quantitative structure-activity relationships
10.1021/ci500747n · 2015 · External reference
The 1,000$ genome, the 100,000$ analysis?
10.1186/gm205 · 2010 · External reference
SeqWare query engine: storing and searching sequence data in the cloud
10.1186/1471-2105-11-s12-s2 · 2010 · External reference
The 100 000 genomes project
10.1136/bmj.i1757 · 2016 · External reference
Speeding up large-scale next generation sequencing data analysis with pBWA
2012 · External reference
SEAL: a distributed short read mapping and duplicate removal tool
10.1093/bioinformatics/btr325 · 2012 · External reference
10.1073/pnas.211566398
10.1073/pnas.211566398 · External reference
10.1038/ng0506-500
10.1038/ng0506-500 · External reference
10.1371/journal.pgen.1005413
10.1371/journal.pgen.1005413 · External reference
NEAT: a framework for building fully automated NGS pipelines and analyses
10.1186/s12859-016-0902-3 · 2016 · External reference
A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data
2015 · External reference
A comprehensive comparison of tools for differential ChIP-seq analysis
2016 · External reference
10.1093/bioinformatics/btp120
10.1093/bioinformatics/btp120 · External reference
10.1038/nbt.1621
10.1038/nbt.1621 · External reference
10.1126/science.1235122
10.1126/science.1235122 · External reference
QuickNGS elevates Next-Generation Sequencing to a new level of automation
10.1186/s12864-015-1695-x · 2015 · External reference
High dimensional biological data retrieval optimization with NoSQL technology
10.1186/1471-2164-15-s8-s3 · 2014 · External reference
Support vector machine-based nomogram predicts postoperative distant metastasis for patients with oesophageal squamous cell carcinoma
10.1038/bjc.2013.379 · 2013 · External reference
An evaluation of copy number variation detection tools for cancer using whole exome sequencing data
10.1186/s12859-017-1705-x · 2017 · External reference
10.1186/gb-2008-9-9-r137
10.1186/gb-2008-9-9-r137 · External reference
