:: DESCRIPTION
ParDRe is a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
ParDRe: Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies.
González-Domínguez J, Schmidt B.
Bioinformatics. 2016 Jan 22. pii: btw038.
:: DESCRIPTION
SPANDx (Synergised Pipeline for Analysis of NGS Data in Linux) is a versatile and customisable tool for the processing of large NGS datasets from raw reads to comparative analysis into a single tool.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Res Notes. 2014 Sep 8;7:618. doi: 10.1186/1756-0500-7-618.
SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets.
Sarovich DS1, Price EP.
:: DESCRIPTION
Cpipe is a variant detection pipeline designed to process high throughput sequencing data (sometimes called “next generation sequencing” data), with the purpose of identifying potentially pathogenic mutations.
::DEVELOPER
the Melbourne Genomics Health Alliance
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Cpipe: a shared variant detection pipeline designed for diagnostic settings.
Sadedin SP, Dashnow H, James PA, Bahlo M, Bauer DC, Lonie A, Lunke S, Macciocca I, Ross JP, Siemering KR, Stark Z, White SM; Melbourne Genomics Health Alliance, Taylor G, Gaff C, Oshlack A, Thorne NP.
Genome Med. 2015 Jul 10;7(1):68. doi: 10.1186/s13073-015-0191-x.
:: DESCRIPTION
bsmooth-align (version 0.8.1). This integrates two different pipelines for aligning WGBS data.
bsseq. This is a R package used for smoothing methylation profiles and identifying DMRs.
bsseqData This is an experiment data package for R, containing an example dataset used in the vignettes (chromosome 21 and 22 from 3 normal colon and 3 colon cancer patients).
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
bsmooth-align, bsseq ,bsseqData
:: MORE INFORMATION
Citation
Genome Biol. 2012 Oct 3;13(10):R83.
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Hansen KD1, Langmead B, Irizarry RA.
:: DESCRIPTION
WGBSSuite is a flexible stochastic simulation tool that generates single-base resolution DNA methylation data genome-wide.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
WGBSSuite: Simulating Whole Genome Bisulphite Sequencing data and benchmarking differential DNA methylation analysis tools.
Rackham OJ, Dellaportas P, Petretto E, Bottolo L.
Bioinformatics. 2015 Mar 15. pii: btv114.
:: DESCRIPTION
OVPDT (Ordered Subset – Variable Threshold – Pedigree Disequilibrium Test) is a family-based association test using both common and rare variants and accounting for directions of effects for sequencing data.
::DEVELOPER
Statistical Genetics and Programming Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2014 Sep 22;9(9):e107800. doi: 10.1371/journal.pone.0107800. eCollection 2014.
Family-based association test using both common and rare variants and accounting for directions of effects for sequencing data.
Chung RH, Tsai WY, Martin ER
:: DESCRIPTION
Lab7 Systems is a team of bioinformaticians, computer scientists, and molecular biologists who are marrying their expertise with a deep knowledge of HPC environments to deliver software solutions that address all aspects of NGS data workflow.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Oct 1;27(19):2648-54. doi: 10.1093/bioinformatics/btr462. Epub 2011 Aug 9.
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF.
:: DESCRIPTION
Wessim is a simulator for a targeted resequencing as generally known as exome sequencing. Wessim basically generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Apr 15;29(8):1076-7. doi: 10.1093/bioinformatics/btt074. Epub 2013 Feb 14.
Wessim: a whole-exome sequencing simulator based on in silico exome capture.
Kim S, Jeong K, Bafna V.
:: DESCRIPTION
Tag-DB provides a user-friendly, lightweight and open-source graphical user interface for running the de novo sequencing algorithm PepNovo+ and also holds the possibiliy to search derived short amino acid sequences (so-called tags) against a protein database in order to retrieve peptide and protein identifications.
::DEVELOPER
Thilo Muth and Harald Barsnes.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION