diCal 1.3 / diCal-IBD 1.0 – Predicts Identical by Descent Tracts using Sequence data

diCal 1.3 / diCal-IBD 1.0

:: DESCRIPTION

diCal is a scalable demographic inference method based on the sequentially Markov conditional sampling distribution framework.

diCal-IBD can be used for predicting identical by descent (IBD) tracts in sequence data. It provides means for calculating the accuracy of the prediction, if the true tracts are available, plotting of the predicted tracts, their TMRCA (time to the most recent common ancestor) and corresponding posterior probabilities, and identification of putative recent positive selection through investigation of average IBD sharing

::DEVELOPER

The Biophysics Graduate Group, Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  diCal-IBD , diCal

:: MORE INFORMATION

Citation

Genetics. 2013 Jul;194(3):647-62. doi: 10.1534/genetics.112.149096. Epub 2013 Apr 22.
Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach.
Sheehan S1, Harris K, Song YS.

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals.
Tataru P, Nirody JA, Song YS.
Bioinformatics. 2014 Aug 21. pii: btu563

KGGSeq 1.2 – Genomic and Genetic studies using Sequence data

KGGSeq 1.2

:: DESCRIPTION

KGGSeq (Genomic and Genetic studies using Sequence data) is a software platform constituted of Bioinformatics and statistical genetics functions making use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants/genes responsible for human diseases/traits. Simply, KGGSeq is like a fishing rod facilitating geneticists to fish the genetic determinants of human diseases/traits in the big sea of DNA sequences. Compared with other genetic tools like plink/seq, KGGSeq paid more attention downstream analysis of genetic mapping. Currently, a comprehensive and efficient framework was newly implemented on KGGSeq to filter and prioritize genetic variants from whole exome sequencing data.

::DEVELOPER

Precision Medicine Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 KGGSeq

:: MORE INFORMATION

Citation

Hum Mutat. 2015 Feb 10. doi: 10.1002/humu.22766.
wKGGSeq: A Comprehensive Strategy-Based and Disease-Targeted Online Framework to Facilitate Exome Sequencing Studies of Inherited Disorders.
Li MJ1, Deng J, Wang P, Yang W, Ho SL, Sham PC, Wang J, Li M.

Li MX, Gui HS, Kwan JS, Bao SY, Sham PC.
A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases.
Nucleic Acids Res. 2012 Jan 12

SeqPop – Compute Population Genetics Statistics on Sequence Data

SeqPop

:: DESCRIPTION

SeqPop is a program for computing population genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

  SeqPop

:: MORE INFORMATION

PRINSEQ 0.20.4 – Preprocess and Generate Statistics about Sequence data

PRINSEQ 0.20.4

:: DESCRIPTION

PRINSEQ (PReprocessing and INformation of SEQuence data.) is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence data. PRINSEQ is available through a user-friendly web interface or as standalone version. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.

PRINSEQ Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 PRINSEQ

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Quality control and preprocessing of metagenomic datasets.
Bioinformatics 2011, 27:863-864.

scan-x 1.1 – Find Motifs within any Sequence data set

scan-x 1.1

:: DESCRIPTION

scan-x is a software tool designed to find motifs within any sequence data set. The first large scale scan was performed using all available human, mouse, fly and yeast phosphorylation and acetylation data to perform a scan for undiscovered modification sites.

::DEVELOPER

Schwartz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2009 Feb;8(2):365-79. doi: 10.1074/mcp.M800332-MCP200. Epub 2008 Oct 28.
Predicting protein post-translational modifications using meta-analysis of proteome scale data sets.
Schwartz D, Chou MF, Church GM.

Curr Protoc Bioinformatics. 2011 Dec;Chapter 13:Unit 13.16.. doi: 10.1002/0471250953.bi1316s36.
Using the scan-x Web site to predict protein post-translational modifications.
Chou MF, Schwartz D.

ASAP 1.1.7 – Automated Sequence data Processing on Computer Clusters

ASAP 1.1.7

:: DESCRIPTION

ASAP (Advanced Sequence Automated Pipeline)is an open source pipeline designed to assist users in managing various jobs associated with processing HiSeq data on a cluster or in serial. . The software was designed to alleviate these issues by providing a modular system to allow users with different needs to process their data with a minimal amount of effort. In addition to minimizing human involvement, ASAP is designed to work on the researcher’s local computer cluster, if one is available

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASAP

:: MORE INFORMATION

Citation

BMC Res Notes. 2013 Jan 4;6:5. doi: 10.1186/1756-0500-6-5.
ASAP: an environment for automated preprocessing of sequencing data.
Torstenson ES1, Li B, Li C.

ReadTools 1.5.2 – Universal Toolkit for Handling Sequence data from different Sequencing Platforms

ReadTools 1.5.2

:: DESCRIPTION

ReadTools provides a consistent and highly tested set of tools for processing sequencing data from any kind of source and focusing on raw reads, while including tools for mapped reads as well.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

ReadTools

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2018 May;18(3):676-680. doi: 10.1111/1755-0998.12741. Epub 2017 Dec 8.
ReadTools: A universal toolkit for handling sequence data from different sequencing platforms.
Gómez-Sánchez D,SchlöttererÇ

verifyBamID 1.1.3 – Identify Contamination of Sample Swap in Sequence data

verifyBamID 1.1.3

:: DESCRIPTION

verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 verifyBamID

:: MORE INFORMATION

Citation

G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang,
Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data,
Am J Hum Genet. 2012 Nov 2;91(5):839-48. doi: 10.1016/j.ajhg.2012.09.004. (volume 91 issue 5 pp.839 – 848)

TrioCaller 20120626 / FamLDCaller 20160215 – LD-aware Genotype Calling and Phasing program for Sequence data

TrioCaller 20120626 / FamLDCaller 20160215

:: DESCRIPTION

TrioCaller is based on a LD-aware method to infer genotypes and phasing for sequencing in trios (or mixed with undrelated individuals).

FamLDCaller is an extension of TrioCaller to handle nuclear and general family structure.

::DEVELOPER

Abecasis Group / Statistical Genetics/Genomes Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TrioCaller  / FamLDCaller

:: MORE INFORMATION

Citation

A computational method for genotype calling in family-based sequencing data.
Chang LC, Li B, Fang Z, Vrieze S, McGue M, Iacono WG, Tseng GC, Chen W.
BMC Bioinformatics. 2016 Jan 16;17(1):37. doi: 10.1186/s12859-016-0880-5.

Genome Res. 2013 Jan;23(1):142-51. doi: 10.1101/gr.142455.112. Epub 2012 Oct 11.
Genotype calling and haplotyping in parent-offspring trios.
Chen W1, Li B, Zeng Z, Sanna S, Sidore C, Busonero F, Kang HM, Li Y, Abecasis GR.

Genome Workbench 2.10.5 – View & Analyze Sequence Data

Genome Workbench 2.10.5

:: DESCRIPTION

Gbench (NCBI Genome Workbench) is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

::DEVELOPER

Genome Workbench Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

Genome Workbench

:: MORE INFORMATION