GENOME 0.2 – Rapid Coalescent-based Whole Genome Simulator

GENOME 0.2

:: DESCRIPTION

GENOME is a program to simulate sequences drawn from a population under the Wright-Fisher neutral model (Ewens 1979). The purpose of this program is to simulate sequences on the whole genome scale within practical time. The program can be used to study the sampling properties of any statistics from a genome-wide study or to evaluate the performance of any method that is applied to genome-wide scale data.

::DEVELOPER

Liming Liang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / SunOS

:: DOWNLOAD

 GENOME

:: MORE INFORMATION

Citation

Liang L., Zollner S., Abecasis G.R. (2006)
GENOME: a rapid coalescent-based whole genome simulator

mRNA by SNP Browser 1.0.1 – Graphical Overviews of Whole-genome Association Study

mRNA by SNP Browser 1.0.1

:: DESCRIPTION

mRNA by SNP Browser” is an interactive package that provides graphical overviews of whole-genome association studies of datasets with very rich phenotypic information, such as global surveys of gene expression. The software incorporates a generic eQTL database and provides a graphic interface for browsing association between 54,675 transcript levels and 406,912 SNPs. For each transcript, our browser can tabulate and plot association test statistics (p-value<0.001), estimates of effect size and allele information across the genome. The browser automatically links results to the UCSC genome browser where users can examine each transcript in its genomic context. In addition to browsing the results by transcript or by position, results can be searched for information on specific SNPs. LD and tag information is provided for SNPs not in our database but evaluated by the International Hapmap Consortium.

::DEVELOPER

Liming Liang

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 mRNA by SNP Browser

:: MORE INFORMATION

Citation

Dixon AL*, Liang L*, Moffatt MF*, Chen W, Heath S, Wong KCC, Taylor J, Gut I, Farrall M, Lathrop GM, Abecasis GR, Cookson WOC (2007).
A genome-wide association study of global gene expression.
Nat Genet 39, 1202-1207 | doi:10.1038/ng2109

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

MethylSig 0.99.4 – Whole Genome DNA Methylation Analysis Pipline

MethylSig 0.99.4

:: 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.

HomologMiner 1.00 – Find Homologous Genomic Groups in Whole Genomes

HomologMiner 1.00

:: DESCRIPTION

HomologMiner is a software to identify homologous groups applicable to genome sequences that have been properly marked for low-complexity repeats and annotated interspersed repeats.

::DEVELOPER

Minmei Hou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 HomologMiner

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Apr 15;23(8):917-25. Epub 2007 Feb 18.
HomologMiner: looking for homologous genomic groups in whole genomes.
Hou M, Berman P, Hsu CH, Harris RS.

BSMAP 2.90 – Whole Genome Bisulfite Sequence MAPping program

BSMAP 2.90

:: DESCRIPTION

BSMAP(Bisulfite Sequence Mapping Program)is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BSMAP

:: MORE INFORMATION

Citation:

BSMAP: whole genome bisulfite sequence MAPping program.
Xi Y, Li W.
BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.

Bioinformatics. 2012 Feb 1;28(3):430-2. doi: 10.1093/bioinformatics/btr668. Epub 2011 Dec 6.
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.
Xi Y, Bock C, Müller F, Sun D, Meissner A, Li W.

DiscoverY – Y-contig Identification from Whole Genome Assemblies

DiscoverY

:: DESCRIPTION

DiscoverY is a tool to shortlist Y-specific contigs from an assembly of male whole genome sequencing data, based on exact k-mer matches with a female.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DiscoverY

:: MORE INFORMATION

Citation:

Rangavittal, S., Stopa, N., Tomaszkiewicz, M. et al.
DiscoverY: A Classifier for Identifying Y Chromosome Sequences in Male Assemblies
BMC Genomics (2019) 20: 641.

PLINK 1.90 b – Whole Genome Association Analysis Toolset

PLINK 1.90 b

:: DESCRIPTION

PLINK is a comprehensive toolset for statistical analysis in whole-genome association studies, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

PLINK

:: MORE INFORMATION

Citation

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007)
PLINK: a toolset for whole-genome association and population-based linkage analysis.
American Journal of Human Genetics, 81.

UnderlyingApproach – Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords

UnderlyingApproach

:: DESCRIPTION

The Underlying Approach (UA) builds a scoring function based on this set of patterns, called underlying. This set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 UnderlyingApproach

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2012 Dec 6;7(1):34. doi: 10.1186/1748-7188-7-34.
Alignment-free phylogeny of whole genomes using underlying subwords.
Comin M, Verzotto D.

wgd – Whole Genome Duplication analysis in Python

wgd

:: DESCRIPTION

wgd is a Python package and command line interface (CLI) for the analysis of whole genome duplications (WGDs). wgd implements methods for constructing Ks distributions starting from a CDS fasta file, tools for intra-genomic synteny analysis and methods for modeling and visualizing Ks distributions.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Python

:: DOWNLOAD

wgd

:: MORE INFORMATION

Citation:

Zwaenepoel, A., and Van de Peer, Y.
wgd – simple command line tools for the analysis of ancient whole genome duplications.
Bioinformatics., bty915, https://doi.org/10.1093/bioinformatics/bty915