Syzygy 1.2.7 – SNP and Indel Calling for pooled and individual Targeted Resequencing Studies

Syzygy 1.2.7

:: DESCRIPTION

Syzygy is a targeted sequencing post processing analysis tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant.

::DEVELOPER

Rivas Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Syzygy

:: MORE INFORMATION

Citation

Rivas et al. (2011),
Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease“,
Nature Genetics 43, 1066–1073 (2011)

LAVA – NGS-based computational SNP Array

LAVA

:: DESCRIPTION

LAVA (Lightweight Assignment of Variant Alleles) is an NGS-based genotyping algorithm for a given set of SNP loci, which takes advantage of the fact that inexact matching of mid-size k-mers (with k = 32) can typically uniquely identify loci in the human genome without full read alignment.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LAVA

:: MORE INFORMATION

Citation:

Ariya Shajii, Deniz Yorukoglu, Yun William Yu, Bonnie Berger;
Fast genotyping of known SNPs through approximate k-mer matching.
Bioinformatics 2016; 32(17): i538-i544. doi: 10.1093/bioinformatics/btw460

FastTagger 1.0 – Genome-Wide Tag SNP selection

FastTagger 1.0

:: DESCRIPTION

FastTagger is a software to calculate multi-marker tagging rules and select tag SNPs based on multi-marker LD. FastTagger uses several techniques to reduce running time and memory consumption.

::DEVELOPER

Limsoon Wong Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux/ Windows
  • C++ Compiler

:: DOWNLOAD

 FastTagger

:: MORE INFORMATION

Citation:

Guimei Liu, Yue Wang, Limsoon Wong.
FastTagger: An Efficient Algorithm for Genome-Wide Tag SNP selection using multi-marker linkage disequilibrium
BMC Bioinformatics, 11:66, February 2010.

MegaSNPHunter – Detect Disease Predisposition SNPs and High Level Interactions

MegaSNPHunter

:: DESCRIPTION

MegaSNPHunter takes case-control genotype data as input and produces a ranked list of multi-SNP interactions. In particular, the whole genome is first partitioned into multiple short subgenomes and a boosting tree classifier is built for each subgenomes based on multi-SNP interactions and then used to measure the importance of SNPs. The method keeps relatively more important SNPs from all subgenomes and let them compete with each other in the same way at the next level. The competition terminates when the number of selected SNPs is less than the size of a subgenome.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MegaSNPHunter

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2009 Jan 9;10:13.
MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study.
Wan X, Yang C, Yang Q, Xue H, Tang NL, Yu W.

atSNP 1.1.2 – Large-scale Testing for SNP-motif Interactions

atSNP 1.1.2

:: DESCRIPTION

atSNP ( Affinity Test for regulatory SNP detection ) package is a bioinformatics tool for computing and testing large-scale motif-SNP interactions.

::DEVELOPER

Chandler Zuo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R

:: DOWNLOAD

atSNP

:: MORE INFORMATION

Citation

atSNP: transcription factor binding affinity testing for regulatory SNP detection.
Zuo C, Shin S, Keleş S.
Bioinformatics. 2015 Jun 18. pii: btv328.

MOCSphaser – Infer Haplotypes composed of Copy Numbers Alleles and SNP Alleles

MOCSphaser

:: DESCRIPTION

MOCSphaser is a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 MOCSphaser

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1645-6. doi: 10.1093/bioinformatics/btn242. Epub 2008 May 20.
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
Kato M1, Nakamura Y, Tsunoda T.

SNP-HWE – Routines for exact SNP tests of Hardy-Weinberg Equilibrium

SNP-HWE

:: DESCRIPTION

SNP-HWE (SNP tests of Hardy-Weinberg Equilibrium) is based on an efficient algorithm for enumerating the exact heterozygote probability distribution conditional on the number of minor alleles present in the sample. It adequately controls Type I error rates within large and small samples and is suitable for use in large-scale studies of SNP data. With appropriate citation, these routines are freely available for your use and can be incorporated into other programs.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • C++ Complier

:: DOWNLOAD

SNP-HWE

:: MORE INFORMATION

Citation:

Wigginton JE, Cutler DJ and Abecasis GR
A Note on Exact Tests of Hardy-Weinberg Equilibrium.
Am J Hum Genet (2005) 76: 887-93

If you decide to use SNP-HWE, please take a minute to register.

MSQT 0.7.3 – Multiple SNP Query Tool

MSQT 0.7.3

:: DESCRIPTION

MSQT is a SNP Query Tool.It was developed to make polymorphism information readily accessible and to assist researchers in selecting distinct sequence changes and developing SNP detection assays.

::DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Perl
  • PostgreSQL

:: DOWNLOAD

 MSQT

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Oct 15;23(20):2784-7. Epub 2007 Sep 4.
MSQT for choosing SNP assays from multiple DNA alignments.
Warthmann N, Fitz J, Weigel D.

eSNPO – SNP Annotation Database and Enrichment analysis platform

eSNPO

:: DESCRIPTION

eSNPO (eQTL based SNP Ontology) is a SNP annotation database and enrichment analysis platform. GWAS is an examination of many common genetic variants in different individuals to see if any variant is associated with a trait. GWASs typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major diseases. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in expression levels of mRNAs. Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Sci Rep. 2016 Jul 29;6:30595. doi: 10.1038/srep30595.
eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform.
Li J, Wang L, Jiang T, Wang J, Li X, Liu X, Wang C, Teng Z, Zhang R, Lv H, Guo M.

PhyloSNP – Take SNP data files (.csv and .vcf) and Generate Phylogenetic Trees

PhyloSNP

:: DESCRIPTION

PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data. Additionally, PhyloSNP can either generate a shortened concatenated genome from the SNPs or generate a concatenated genome from contigs generated from the SNPs and a specified number of base pairs around each SNP.

::DEVELOPER

High-performance Integrated Virtual Environment (HIVE)

:: SCREENSHOTS

PhyloSNP

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

  PhyloSNP

:: MORE INFORMATION

Citation

Genomics. 2014 Jul;104(1):1-7. doi: 10.1016/j.ygeno.2014.06.001. Epub 2014 Jun 12.
Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes.
Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R