Ehapp – Estimate Haplotype Frequency from Pooled Sequencing data

Ehapp

:: DESCRIPTION

Taking advantage of prior haplotype database, Ehapp implements lsqnonneg and GPSR algrithm to estimate the frequencies of haplotypes from pooled sequencing data.

::DEVELOPER

Bioinfomatics Lab of SouthEast Universtity

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Ehapp

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 9. pii: btu670.
Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing.
Cao CC1, Sun X

extraBinomial 2.1 – Extra-binomial Approach for Pooled Sequencing data

extraBinomial 2.1

:: DESCRIPTION

extraBinomial tests for differences in minor allele frequency between groups and is based on an extra-binomial variation model for pooled sequencing data.

::DEVELOPER

Xin Yang <xin.yang at cimr.cam.ac.uk>, Chris Wallace

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 extraBinomial

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2898-904. doi: 10.1093/bioinformatics/bts553. Epub 2012 Sep 12.
Extra-binomial variation approach for analysis of pooled DNA sequencing data.
Yang X1, Todd JA, Clayton D, Wallace C.

PoolHap2 1.0.0 – Inferring Haplotype frequencies from Pooled Sequencing

PoolHap2 1.0.0

:: DESCRIPTION

PoolHap2 is a computer program that infers haplotype (or epitype in case of DNA methylation sequencing) from a pool.  In its current release, only pathogen sequencing application is implemented. In pathogen studies utilizing next generation sequencing, investigators ofte n collect samples naturally as pools of multiple strains, e.g., when the samples are taken from patients’ blood. To analyze these types of within-host polymorphisms, one would ideally like to determine the haplotypes in the sample. Even though isolation of single strains is possible by time-consuming experiments, the haplotype frequencies of different pathogen strains within a host are usually unknown, and this may well alter the initial within-sample frequencies. Here we developed Poolhap, a tool enabling researchers to infer the strain numbers and haplotype frequencies in silico from sequences of pooled samples.

::DEVELOPER

Quan Long

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java

:: DOWNLOAD

 PoolHap

:: MORE INFORMATION

Citation

PLoS One. 2011 Jan 5;6(1):e15292. doi: 10.1371/journal.pone.0015292.
PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing.
Long Q, Jeffares DC, Zhang Q, Ye K, Nizhynska V, Ning Z, Tyler-Smith C, Nordborg M.

Psafe 20120530 – Pooled Sequencing Allele Frequency Estimation

Psafe 20120530

:: DESCRIPTION

Psafe is a pipeline to adjust the biases and errors of sequencing data to gain more accurate allele frequency estimation.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/MacOsX
  • Perl

:: DOWNLOAD

 Psafe

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 Sep;36(6):549-60. doi: 10.1002/gepi.21648. Epub 2012 Jun 6.
Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples.
Chen X, Listman JB, Slack FJ, Gelernter J, Zhao H.