HARSH 0.21 – Haplotype Inference using Reference and Sequencing Data

HARSH 0.21

:: DESCRIPTION

HARSH (HAplotype inference using Reference and Sequencing tecHnology) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 HARSH

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386.
Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.
Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

SNPYGoat 1.0 – Identify Several Goat Y-chromosomal Haplotypes

SNPYGoat 1.0

:: DESCRIPTION

SNPYGoat Software allows users of the SNPYGoat multiplex system to rapidly identify several goat Y-chromosomal haplotypes  Y1A, Y1B, Y1C and Y2 by automatically comparing the obtained profile with a reference database.

::DEVELOPER

Filipe Pereira

:: SCREENSHOTS

: REQUIREMENTS

  • Windows

:: DOWNLOAD

SNPYGoat

:: MORE INFORMATION

Citation

Pereira F, Carneiro J, Soares P, Maciel S, Nejmeddine F, Lenstra JA, Gusm?o L, Amorim A
A multiplex primer extension assay for the rapid identification of paternal lineages in domestic goat (Capra hircus): laying the foundations for a detailed caprine Y chromosome phylogeny
Molecular Phylogenetics and Evolution. 2008. 49:663-668

HapYDive – Excel Plugin for Y-STR Haplotype Diversity Calculation

HapYDive

:: DESCRIPTION

HapYDive is a software for Y-STR haplotype diversity calculation.This program allows fast and reliable determination of which Y-STRs are the most informative by evaluating all possible combinations.With the HapYDive it is possible to analyse any set of Y markers up to a maximum of 20, with a minimum number of 4 markers fixed for calculations. Results on the application of this program to different population samples and sizes and with a certain combination of Y-STR markers are presented and discussed, together with its usefulness mainly to the forensic community.

::DEVELOPER

Filipe Pereira

:: SCREENSHOTS

: REQUIREMENTS

  • Windows
  • Excel

:: DOWNLOAD

HapYDive

:: MORE INFORMATION

Citation

Alves C, Gusmão L, Meirinhos J, Amorim A (2006)
Making the most of Y-STR haplotypes. The HapYDive.
Forensic Genetics 11: 201-203.

HapCompass 0.8.2 – A Cycle-Basis Algorithm for Accurate Haplotype Assembly

HapCompass 0.8.2

:: DESCRIPTION

HapCompass for polyploid genomes can currently be used to create accurate pairwise SNP phasings.Given a set of aligned sequence reads in a SAM file and a set of variant calls in VCF format, HAPCOMPASS will assemble reads into haplotypes.

::DEVELOPER

The Istrail Laboratory of Brown University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 HapCompass

:: MORE INFORMATION

Citation

HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data.
Aguiar D, Istrail S.
J Comput Biol. 2012 Jun;19(6):577-90. doi: 10.1089/cmb.2012.0084.

LocHap 2.0 – Local-Haplotype Variant Calling Software

LocHap 2.0

:: DESCRIPTION

LocHap is an ultra-fast computational pipeline for calling local haplotype variant using deep DNA-sequencing data to reveal cellular heterogeneity and somatic mosaicism.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 LocHap

:: MORE INFORMATION

Citation

Sengupta S, Gulukota K, Zhu Y, Ober C, Naughton K, Wentworth-Sheilds W, Ji Y.
Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples.
Nucleic Acids Res. 2016 Feb 18;44(3):e25. doi: 10.1093/nar/gkv953. Epub 2015 Sep 29. PMID: 26420835; PMCID: PMC4756850.

LDExplorer 1.0.3 – Whole-genome LD-based Haplotype Block Recognition

LDExplorer 1.0.3

:: DESCRIPTION

LDExplorer is an R package for the memory efficient whole-genome LD-based haplotype block recognition.

::DEVELOPER

the Center of Biomedicine (CBM) at EURAC research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • R package 

:: DOWNLOAD

LDExplorer

:: MORE INFORMATION

hapsembler 2.21 – Haplotype-specific Genome Assembly Toolkit

hapsembler 2.21

:: DESCRIPTION

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  hapsembler

:: MORE INFORMATION

Citation

Nilgun Donmez and Michael Brudno (2011)
Hapsembler: an assembler for highly polymorphic genomes.
In Proceedings of the 15th Annual international conference on Research in computational molecular biology (RECOMB’11), Springer-Verlag, Berlin, Heidelberg, 38-52.

ShoRAH v1.9.95 – Short Reads Assembly into Haplotypes

ShoRAH v1.9.95

:: DESCRIPTION

ShoRAH is a software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ShoRAH

:: MORE INFORMATION

Citation

Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N (2011)
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
BMC Bioinformatics, vol. 12 p. 119

FamLBL 1.0 – Detecting Rare Haplotype Disease Association Based on Common SNPs Using Case-Parent Triads

FamLBL 1.0

:: DESCRIPTION

famLBL (family-triad-based logistic Bayesian Lasso) is an R package for estimating effects of haplotypes on complex diseases using SNP data.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FamLBL

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 21. pii: btu347. [Epub ahead of print]
FamLBL: Detecting Rare Haplotype Disease Association Based on Common SNPs Using Case-Parent Triads.
Wang M1, Lin S2.

HapTree-X v1.0 – Haplotype Reconstruction tool Tailored towards RNA-seq Reads

HapTree-X v1.0

:: DESCRIPTION

HapTree-X is a haplotype reconstruction tool tailored towards phasing experiments with RNA-seq reads (by itself or jointly with genome/exome sequencing reads).

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HapTree-X

:: MORE INFORMATION

Citation:

Res Comput Mol Biol, 9029, 28-29 2015
HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction From Transcriptome and Genome Sequencing Data
Emily Berger, Deniz Yorukoglu, Bonnie Berger