SGRP – Saccharomyces Genome Resequencing Project

SGRP

:: DESCRIPTION

SGRP is a collaborative project to explore genetic and phenotypic diversity of Saccharomyces.

::DEVELOPER

Alan Moses’ Computational Biology Lab,University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

MP

:: MORE INFORMATION

Citation

Mol Biol Evol. 2014 Apr;31(4):872-88. doi: 10.1093/molbev/msu037. Epub 2014 Jan 14.
A high-definition view of functional genetic variation from natural yeast genomes.
Bergström A1, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G.

TASUKE ver.20190826 – Visualization program for Large-scale Resequencing data

TASUKE ver.20190826

:: DESCRIPTION

TASUKE is a web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies.The variation and read depth of multiple genomes, as well as annotations, can be shown simultaneously at various scales.

::DEVELOPER

Bioinformatics Research Unit, Agrogenomics Research Center

:: SCREENSHOTS

TASUKE

:: REQUIREMENTS

  • Linux
  • Apach
  • Php
  • MySQL

:: DOWNLOAD

 TASUKE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 15;29(14):1806-8. doi: 10.1093/bioinformatics/btt295. Epub 2013 Jun 7.
TASUKE: a web-based visualization program for large-scale resequencing data.
Kumagai M1, Kim J, Itoh R, Itoh T.

BFC – High-performance Error Correction for Illumina Resequencing data

BFC v1

:: DESCRIPTION

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BFC

:: MORE INFORMATION

Citation

Bioinformatics. 2015 May 6. pii: btv290.
BFC: correcting Illumina sequencing errors.
Li H

bamchop – Generate Targeted Resequencing Report from BAM File

bamchop

:: DESCRIPTION

bamchop is a robust program to efficiently summarize key statistical metrics of HTS data stored in BAM files, and to visually present the results in a formatted report.

::DEVELOPER

The Department of Biomedical and Health Informatics (DBHi)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • R
  • LaTeX

:: DOWNLOAD

 bamchop

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013;14 Suppl 11:S3. doi: 10.1186/1471-2105-14-S11-S3. Epub 2013 Sep 13.
Efficient digest of high-throughput sequencing data in a reproducible report.
Zhang Z, Leipzig J, Sasson A, Yu AM, Perin JC, Xie HM, Sarmady M, Warren PV, White PS.

Optimus Primer – Primer Design for large-scale Resequencing by Second Generation Sequencing

Optimus Primer

:: DESCRIPTION

Optimus Primer is a PCR enrichment primer design program for next-generation sequencing of human exonic regions.

::DEVELOPER

Laboratory of Guillaume Lettre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Res Notes. 2010 Jul 7;3:185. doi: 10.1186/1756-0500-3-185.
Optimus Primer: A PCR enrichment primer design program for next-generation sequencing of human exonic regions.
Brown AM, Lo KS, Guelpa P, Beaudoin M, Rioux JD, Tardif JC, Phillips MS, Lettre G.

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

the Broad Institute of MIT and Harvard

:: 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)

SeqAlto 0.5-r123 – Fast and Accurate Read Alignment for Resequencing

SeqAlto 0.5-r123

:: DESCRIPTION

 SeqAlto is an aligner specifically designed for Illumina reads of length greater or equal to about 100-bp. It takes advantage of this longer read length to provide fast alignment rates and accurate placement of polymorphic reads. Paired-end reads are recommended for even greater accuracy. When aligning 100-bp paired-end reads SeqAlto is on average about 2-4x faster than BWA while being more sensitive and much faster for longer reads.

::DEVELOPER

Wong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/  Linux

:: DOWNLOAD

 SeqAlto

:: MORE INFORMATION

Citation

John C. Mu, Hui Jiang, Amirhossein Kiani, Marghoob Mohiyuddin, Narges Bani Asadi and Wing H. Wong,
Fast and Accurate Read Alignment for Resequencing,
Bioinformatics (2012) 28 (18): 2366-2373.