GLAPD – Whole Genome based LAMP Primer Design for a set of Target Genome

GLAPD

:: DESCRIPTION

GLAPD can design LAMPP(Loop-mediated isothermal amplification) primer sets based on a whole genome. It can also design LAMP primers for a set of target genomes. Users can specify a group of background genomes.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Bowtie
  • CUDA driver

:: DOWNLOAD

GLAPD

:: MORE INFORMATION

MethylExtract 1.9.1 – Methylation Maps and SNV calling from Whole Genome Bisulfite Sequencing Data

MethylExtract 1.9.1

:: DESCRIPTION

MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MethylExtract

:: MORE INFORMATION

Citation

Version 2. F1000Res. 2013 Oct 15 [revised 2014 Feb 21];2:217. doi: 10.12688/f1000research.2-217.v2. eCollection 2013.
MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data.
Barturen G, Rueda A, Oliver JL, Hackenberg M.

kSNP 3.1.2 – SNP Discovery and SNP Annotation from Whole Genomes

kSNP 3.1.2

:: DESCRIPTION

kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

kSNP

:: MORE INFORMATION

Citation

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome.
Gardner SN, Slezak T, Hall BG.
Bioinformatics. 2015 Sep 1;31(17):2877-8. doi: 10.1093/bioinformatics/btv271.

PLoS One. 2013 Dec 9;8(12):e81760. doi: 10.1371/journal.pone.0081760. eCollection 2013.
When whole-genome alignments just won’t work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.
Gardner SN, Hall BG.

WhopGenome 0.9.7 – High-speed Access to Whole-genome Variation Data

WhopGenome 0.9.7

:: DESCRIPTION

WhopGenome is a package for R that provides high-speed access to Variant Call Format (VCF) files as e.g. published by the 1000 Genomes Project.. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.

::DEVELOPER

Computational Cell Biology,   Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows  / MacOsX
  • R

:: DOWNLOAD

 WhopGenome

:: MORE INFORMATION

Citation

WhopGenome: high-speed access to whole genome variation and sequence data in R.
Wittelsbürger U, Pfeifer B, Lercher MJ.
Bioinformatics. 2015 Feb 1;31(3):413-5. doi: 10.1093/bioinformatics/btu636

MethGo – Analyzing Whole-genome Bisulfite Sequencing data

MethGo

:: DESCRIPTION

MethGo is a simple and effective tool designed for the analysis of data from whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS).

::DEVELOPER

Pao-Yang Chen’s Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MethGo

:: MORE INFORMATION

Citation

MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data.
Liao WW, Yen MR, Ju E, Hsu FM, Lam L, Chen PY.
BMC Genomics. 2015 Dec 9;16 Suppl 12:S11. doi: 10.1186/1471-2164-16-S12-S11.

bsmooth-align 0.8.1 – Analyzing Whole Genome Bisulfite Sequencing (WGBS) data

bsmooth-align

:: 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

RafaLab, Hansen Lab

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

 bsmooth-alignbsseq ,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.

WGBSSuite 0.4 – Simulating Whole Genome Bisulphite Sequencing data

WGBSSuite 0.3

:: DESCRIPTION

WGBSSuite is a flexible stochastic simulation tool that generates single-base resolution DNA methylation data genome-wide.

::DEVELOPER

WGBSSuite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Bsmooth
  • MethylSig

:: DOWNLOAD

  WGBSSuite

:: 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.

MethylSig 0.4.3 – Whole Genome DNA Methylation Analysis Pipline

MethylSig 0.4.3

:: DESCRIPTION

MethylSig is our new R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced representation bisulfite sequencing (RRBS), or enhanced RRBS experiments. Methylsig tests for differentially methylated sites (DMCs) or regions (DMRs) using a beta-binomial model to account for the coverage and variation among samples at each CpG site or region, and has a well-calibrated Type 1 error rate. Several options exist for either site-specific or sliding window tests, combining strands, filtering sites, and for local variance estimation. In addition, methylSig offers numerous functions for annotating and visualizing results, and testing for enrichment of overlap with the binding sites of transcription factors.

::DEVELOPER

The Sartor Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 MethylSig

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 16. pii: btu339. [Epub ahead of print]
methylSig: a whole genome DNA methylation analysis pipeline.
Park Y1, Figueroa ME1, Rozek LS2, Sartor MA3.

SomaticSniper 1.0.5 – Somatic SNV Detection for Whole Genome Resequencing Data.

SomaticSniper 1.0.5

:: DESCRIPTION

SomaticSniper is a software for comparing tumor and normal pairs. The developer estimate its sensitivity and precision, and present several common sources of error resulting in miscalls.

::DEVELOPER

The Genome Institute at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 SomaticSniper

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Feb 1;28(3):311-7.
SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data.
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L.

LDExplorer 1.0.3 – Whole-genome LD-based Haplotype Block Recognition

LDExplorer 1.0.3

:: DESCRIPTION

LDExplorer is an R package for the memory efficient whole-genome LD-based haplotype block recognition.

::DEVELOPER

the Center of Biomedicine (CBM) at EURAC research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • R package 

:: DOWNLOAD

LDExplorer

:: MORE INFORMATION