PoolHap2 1.0.0 – Inferring Haplotype frequencies from Pooled Sequencing

PoolHap2 1.0.0


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.



Quan Long




  • Linux/ Windows / MacOsX
  • Java





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.