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.

KGGSeq 1.1 / wKGGSeq 20150119 – Genomic and Genetic studies using Sequence data

KGGSeq 1.1 / wKGGSeq 20150119

:: 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.

wKGGSeq is a framework facilitating comprehensive downstream analysis of next-generation sequencing data to identify causal mutation of human diseases for basic research and clinic diagnosis.

::DEVELOPER

Miao-xin Li, JJWang Lab

:: 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

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

CHIAMANTE 1.0.3 – Joint Genotype Calling algorithm for Array and Sequence data

CHIAMANTE 1.0.3

:: DESCRIPTION

Chiamante is a genotype caller for Illumina Beadchips that can augment microarray data with genotype likelihoods from sequence data for improved genotype accuracy and call rate. Whilst primarily designed to call genotypes via fusing these two sources of information, Chiamante also functions as a highly accurate array-only caller.

::DEVELOPER

Jared O’Connell and Jonathan Marchini.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CHIAMANTE

:: MORE INFORMATION

Citation

J O’Connell, J. Marchini (2012)
Joint Genotype Calling With Array and Sequence Data.
Genetic Epidemiology. 10.1002/gepi.21657

SeqToolBox 0.02 – A set of Perl modules and scripts for Operations on Sequence data

SeqToolBox 0.02

:: DESCRIPTION

SeqToolBox is a set of Perl modules and scripts for day to day operations on sequence data. Includes, parsers for standard file formats and some utility modules, such as modules for working with “sets”, a set of modules for handling NCBI taxonomy database etc. The bin directory contains some scripts to run jobs on clusters.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  SeqToolBox

:: MORE INFORMATION

FastQC 0.11.5 – Quality Control Tool for High Throughput Sequence Data

FastQC 0.11.5

:: DESCRIPTION

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java 

:: DOWNLOAD

 FastQC

:: MORE INFORMATION

SequenceServer 1.0.6 – Set up a Local BLAST Web Server to Search & Share Sequence data

SequenceServer 1.0.6

:: DESCRIPTION

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.

::DEVELOPER

Wurm Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SequenceServer

:: MORE INFORMATION

Citation

Sequenceserver: a modern graphical user interface for custom BLAST databases
Anurag Priyam, Ben J Woodcroft, Vivek Rai, Alekhya Munagala, Ismail Moghul, Filip Ter, Mark Anthony Gibbins, HongKee Moon, Guy Leonard, Wolfgang Rumpf, Yannick Wurm
doi: http://dx.doi.org/10.1101/033142

ClonalFrame 1.2 / ClonalFrameML 1.0 – Inference of Bacterial Microevolution using Multilocus Sequence data

ClonalFrame 1.2 / ClonalFrameML 1.0

:: DESCRIPTION

ClonalFrame is a computer package for the inference of bacterial microevolution using multilocus sequence data.In a nutshell, ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, we recommend using Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.

ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes.

::DEVELOPER

Xavier Didelot and Daniel Wilson

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 ClonalFrame , ClonalFrameML

:: MORE INFORMATION

Citation

ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Didelot X, Wilson DJ.
PLoS Comput Biol. 2015 Feb 12;11(2):e1004041. doi: 10.1371/journal.pcbi.1004041.

Didelot and Falush (2007)
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Genetics March 2007 vol. 175 no. 3 1251-1266

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