Satsuma2 – Whole-genome Synteny Aligner

Satsuma2

:: DESCRIPTION

Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences.

Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accomodate the billions of base pairs in vertebrate genomes).

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
C++ Compiler

:: DOWNLOAD

Satsuma2

:: MORE INFORMATION

Citation

Grabherr MG, Russell P, Meyer M, Mauceli E, Alfoldi J, Di Palma F, Lindblad-Toh K.
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Bioinformatics. 2010 May 1;26(9):1145-51. Epub 2010 Mar 5

Atlas 2005 – Whole Genome Assembly Suite

Atlas 2005

:: DESCRIPTION

Atlas is a collection of software tools to facilitate the assembly of large genomes from whole genome shotgun reads, or a combination of whole genome shotgun reads and BAC or other localized reads.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Atlas

:: MORE INFORMATION

SampleSeq and SampleSeq2 – Optimal Subject Selection in Targeted and Whole Genome Sequencing Experiments

SampleSeq and SampleSeq2

:: DESCRIPTION

SampleSeq is a probability-based algorithm for selecting samples for a targeted resequencing experiment.

SampleSeq2 requires a squared matrix of pairwise distance among all subjects that are candidates for selection. The matrix can be generated by PLINK using GWAS data or by Idcoefs using pedigree information. These are explained in detail in Sections II and III.In Section IV, we describe how to use SampleSeq2 for subject selection. In Section V, we describe how to estimate the number of independent genomes in a subset of subjects.

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R package
Perl

:: DOWNLOAD

SampleSeq

:: MORE INFORMATION

Citation

Edwards TL, Li C (2012)
Optimized selection of unrelated subjects for whole genome sequencing studies of rare high-penetrance alleles.
Genet Epidemiol. 2012 Jul;36(5):472-9. doi: 10.1002/gepi.21641. Epub 2012 May 23.

GWAsimulator 2.1 – Rapid Whole Genome Simulation program

GWAsimulator 2.1

:: DESCRIPTION

GWAsimulator is a C++ program that can simulate genotype data for SNP chips that are used in genome-wide association (GWA) studies. It implements a rapid moving-window algorithm (Durrant et al. 2004. AJHG 75:35-43) to simulate whole genome case-control or population samples. It also can simulate specific regions if desired. For case-control data, the program retrospectively sample cases and controls according to a user-specified multi-locus disease model. The program requires phased data as input, and the simulated data will have similar LD patterns as the input data.

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

GWAsimulator

:: MORE INFORMATION

Citation

Li C, Li M (2008)
GWAsimulator: A rapid whole genome simulation program.
Bioinformatics 24:140-142

MaSuRCA 4.0.4 – Whole Genome Short Read Assembler

MaSuRCA 4.0.4

:: DESCRIPTION

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).

::DEVELOPER

IPST GENOME ASSEMBLY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MaSuRCA

:: MORE INFORMATION

Citation

The MaSuRCA genome assembler.
Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA.
Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476.

Metassembler 1.5 – Combines multiple Whole Genome de novo Assemblies into a combined Consensus Assembly

Metassembler 1.5

:: DESCRIPTION

Metassembler is a software package for reconciling assemblies produced by de novo short-read assemblers such as SOAPdenovo and ALLPATHS-LG. The goal of assembly reconciliation, or “metassembly,” is to combine multiple assemblies into a single genome that is superior to all of its constituents

::DEVELOPER

Schatz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Metassembler

:: MORE INFORMATION

Citation

Genome Biol. 2015 Sep 24;16:207. doi: 10.1186/s13059-015-0764-4.
Metassembler: merging and optimizing de novo genome assemblies.
Wences AH, Schatz MC

Alignathon – Multiple Whole Genome Alignment Testing Suite

Alignathon

:: DESCRIPTION

The Alignathon is a collaborative competition to assess the state of the art in whole genome sequence alignment.

::DEVELOPER

Dent Earl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Python

:: DOWNLOAD

Alignathon

:: MORE INFORMATION

Citation

Alignathon: A competitive assessment of whole genome alignment methods.
Earl D, et al.
Genome Res. 2014 Oct 1. pii: gr.174920.114.

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.

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