:: DESCRIPTION
HomSI is a homozygous stretch identifier from next-generation sequencing data.
::DEVELOPER
Advanced Genomics and Bioinformatic Research Group, İGBAM
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Feb 1;30(3):445-7. doi: 10.1093/bioinformatics/btt686. Epub 2013 Dec 3.
HomSI: a homozygous stretch identifier from next-generation sequencing data.
Görmez Z1, Bakir-Gungor B, Sagiroglu MS.
:: DESCRIPTION
VirusScan pipeline is a fully automated and modular software package designed for the fast and accurate detection of known viruses from NGS data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R 3rd, Johnson KJ, Gay H, Chen K, Rader JS, Dipersio JF, Chen F, Ding L.
Divergent viral presentation among human tumors and adjacent normal tissues.
Sci Rep. 2016 Jun 24;6:28294. doi: 10.1038/srep28294. PMID: 27339696; PMCID: PMC4919655.
:: DESCRIPTION
Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of “seq2gene” and “gene2path” components.
::DEVELOPER
Xinan Yang <xyang2 at uchicago.edu>; Bin Wang <binw at uchicago.edu>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.
Wang B, Cunningham JM, Yang XH.
Bioinformatics. 2015 May 15. pii: btv289
:: DESCRIPTION
ngs.plot is an easy-to-use visualization tool for global enrichment of next-generation sequencing data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Shen, L., Shao, N., Liu, X. and Nestler, E. (2014)
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.
BMC Genomics. 2014 Apr 15;15(1):284. doi: 10.1186/1471-2164-15-284.
:: DESCRIPTION
FusionMap is an efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Jul 15;27(14):1922-8. Epub 2011 May 18.
FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.
Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W.
:: DESCRIPTION
KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform. It has recently been updated with new functionality and workflows that open the door to performing next generation sequencing analysis using the KNIME framework.
::DEVELOPER
(bernd.jagla@pasteur.fr) Departement Génomes et Génétique, Institut Pasteur
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Oct 15;27(20):2907-9. doi: 10.1093/bioinformatics/btr478. Epub 2011 Aug 27.
Extending KNIME for next-generation sequencing data analysis.
Jagla B, Wiswedel B, Coppée JY.
:: DESCRIPTION
TreeClone is a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
[Submitted on 10 Mar 2017 (v1), last revised 25 Oct 2017 (this version, v2)]
TreeClone: Reconstruction of Tumor Subclone Phylogeny Based on Mutation Pairs using Next Generation Sequencing Data
Tianjian Zhou, Subhajit Sengupta, Peter Mueller, Yuan Ji
:: DESCRIPTION
ngCGH computes a pseudo-CGH using simple coverage counting on the tumor relative to the normal.
::DEVELOPER
Sean Davis @NCI
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The IntSim software package has been developed to simulate various genome mutations including germline and somatic variations from next generation sequencing data, and also to generate read data from mixed genomes by considering moderate levels of tumor purity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
IntSIM: An Integrated Simulator of Next-Generation Sequencing Data.
Yuan X, Zhang J, Yang L.
IEEE Trans Biomed Eng. 2016 Apr 29.
:: DESCRIPTION
SVGen is a tool with an extensive range of options to simulate germline and somatic SVs of various types and from short and long read sequencing platforms. The output from SVGen include BED files with SV regions, FASTA files with the simulated genome sequence and FASTQ files for short or long reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
LA Lima, H Yang, C Dong, K Wang.
SVGen: Simulation of structural variants in next-generation sequencing data.
(submitted)
