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

HapTree 1.0 – Polyploid Haplotype Assembly tool

HapTree 1.0

:: DESCRIPTION

HapTree is a polyploid haplotype assembly tool based on a statistical framework.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  HapTree

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2014 Mar 27;10(3):e1003502. doi: 10.1371/journal.pcbi.1003502. eCollection 2014.
HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data.
Berger E, Yorukoglu D, Peng J, Berger B

CNVphaser / CNVphaserPro 1.1 – Infer CNV Haplotypes with Variations

CNVphaser / CNVphaserPro 1.1

:: DESCRIPTION

CNVphaser infers haplotypes with variations in both copy numbers and nucleotide sequences within a CNV region

CNVphaserPro, a successor of CNVphaser and MOCSphaser to handle noisy CNV data such as microarray data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 CNVphaser / CNVphaserPro

:: MORE INFORMATION

Citation

Am J Hum Genet. 2008 Aug;83(2):157-69. doi: 10.1016/j.ajhg.2008.06.021. Epub 2008 Jul 17.
An algorithm for inferring complex haplotypes in a region of copy-number variation.
Kato M1, Nakamura Y, Tsunoda T.

ParaHaplo 4.0 beta – Tools for Haplotype-based Whole-genome Association Study using Parallel Computing

ParaHaplo 4.0 beta

:: DESCRIPTION

ParaHaplo is developing parallel computing tools for genome-wide association studies.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • OpenMPI version 1.2.5, or MPICH version 1.2.7p1

:: DOWNLOAD

 ParaHaplo

:: MORE INFORMATION

Citation

ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing.
Misawa K, Kamatani N.
Source Code Biol Med. 2011 May 24;6(1):10. doi: 10.1186/1751-0473-6-10.

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.

FUGUE 0.2.3 – Haplotype Frequency Estimation

FUGUE 0.2.3

:: DESCRIPTION

FUGUE is the program used to construct haplotypes for the chromosome and linkage disequilibrium maps.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • MERLIN

:: DOWNLOAD

FUGUE

:: MORE INFORMATION

Citation:

Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR and Dunham I
A first-generation linkage disequilibrium map of human chromosome
Nature (2002) 418:544-548

Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT and Cardon LR
Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots.
Nat Genet (2003) 33:382-7

MACH 1.0 – Haplotyping, Genotype Imputation & Disease Association Analysis

MACH 1.0

:: DESCRIPTION

MACH (Markov Chain Haplotyping) is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

MACH

:: MORE INFORMATION

Citation:

Li Y, Willer CJ, Ding J, Scheet P and Abecasis GR (2006)
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes.
Genet Epidemiol 34:816-834.

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