:: DESCRIPTION
gCUP: Rapid GPU-based HIV-1 Coreceptor Usage Prediction for Next-Generation Sequencing
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
gCUP: Rapid GPU-based HIV-1 Co-Receptor Usage Prediction for Next-Generation Sequencing.
Olejnik M, Steuwer M, Gorlatch S, Heider D.
Bioinformatics. 2014 Aug 13. pii: btu535.
:: DESCRIPTION
Pooling is a computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling
::DEVELOPER
Georgia State University NGS Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Computational Framework for Next-Generation Sequencing of Heterogeneous Viral Populations using Combinatorial Pooling.
Skums P, Artyomenko A, Glebova O, Ramachandran S, Mandoiu I, Campo DS, Dimitrova Z, Zelikovsky A, Khudyakov Y.
Bioinformatics. 2014 Oct 29. pii: btu726.
:: DESCRIPTION
PriVar is a cross-platform Java application toolkit to prioritize variants (SNVs and InDels) from exome or whole genome sequencing data by using different filtering strategies and information of external databases.
::DEVELOPER
WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Jan 1;29(1):124-5. doi: 10.1093/bioinformatics/bts627. Epub 2012 Oct 25.
PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data.
Zhang L1, Zhang J, Yang J, Ying D, Lau YL, Yang W.
:: DESCRIPTION
ICC (Indel and Carryforward Correction) is a software pipeline to analyze 454 pyrosequencing data, including read quality filtering and alignment, indel and carryforward error correction, single nucleotide variant calling, and calculation of nucleotide variant and hyplotype frequencies.
::DEVELOPER
Mullins Molecular Retrovirology Lab, University of Washington.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Oct 1;29(19):2402-9. doi: 10.1093/bioinformatics/btt434. Epub 2013 Jul 29.
Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.
Deng W1, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI.
:: DESCRIPTION
StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
F1000Research 2014, 2:248 (doi: 10.12688/f1000research.2-248.v2)
StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.
Ramirez-Gonzalez RH, Leggett RM, Waite D, Thanki A, Drou N, Caccamo M, Davey R
:: DESCRIPTION
Omics pipe is an open-source, modular computational platform that automates best practice multi-omics data analysis pipelines published in Nature Protocols and other commonly used pipelines, such as GATK.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Omics Pipe: A Community-based Framework for Reproducible Multi-Omics Data Analysis.
Fisch KM, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI.
Bioinformatics. 2015 Jan 30. pii: btv061.
:: DESCRIPTION
NGS++ is a programming library in C++11 specialized in manipulating both next-generation sequencing (NGS) datasets and genomic information files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Aug 1;29(15):1893-4. doi: 10.1093/bioinformatics/btt312. Epub 2013 Jun 4.
NGS++: a library for rapid prototyping of epigenomics software tools.
Nordell Markovits A1, Joly Beauparlant C, Toupin D, Wang S, Droit A, Gevry N.
:: DESCRIPTION
GenomeJack is a genome browser specialized in next-generation sequencing data.
::DEVELOPER
MITSUBISHI SPACE SOFTWARE CO.,LTD
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mult Scler. 2013 Jul;19(8):1035-45. doi: 10.1177/1352458512471873.
Molecular network of chromatin immunoprecipitation followed by deep sequencing-based vitamin D receptor target genes.
Satoh J, Tabunoki H.
:: DESCRIPTION
ViQuaS is based on a novel reference-assisted de novo assembly algorithm for constructing local haplotypes. A significantly extended version of an existing global strain reconstruction algorithm is also used.
::DEVELOPER
Duleepa Jayasundara <d.jayasundara@student.unimelb.edu.au>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
ViQuaS: An improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing.
Jayasundara D, Saeed I, Maheswararajah S, Chang BC, Tang SL, Halgamuge SK.
Bioinformatics. 2015 Mar 15;31(6):886-96. doi: 10.1093/bioinformatics/btu754
:: DESCRIPTION
Goby is a next-generation sequencing data management framework designed to facilitate the implementation of efficient data analysis pipelines.
GobyWeb is a web application to aid with the analysis of high-throughput sequencing (HTS) data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013 Jul 23;8(7):e69666. doi: 10.1371/journal.pone.0069666. Print 2013.
GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data.
Dorff KC, Chambwe N, Zeno Z, Simi M, Shaknovich R, Campagne F.
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