PoolHap2 / PoolHapX 1.0.0 – Inferring Haplotype frequencies from Pooled Sequencing

PoolHap2 / PoolHapX 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.


The PoolHapX program reconstructs haplotypes within-host from pooled-sequencing data by integrating population genetic models (statistical linkage disequilibrium) with genomics reads (physical linkage). It approximate the resolution of single-cell sequencing using only pooled sequencing data, enabling within-host evolution analyses.


Quan Long




  • Linux/ Windows / MacOsX
  • Java


 PoolHap , PoolHapX



Cao C, He J, Mak L, Perera D, Kwok D, Wang J, Li M, Mourier T, Gavriliuc S, Greenberg M, Morrissy AS, Sycuro LK, Yang G, Jeffares DC, Long Q.
Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding.
Mol Biol Evol. 2021 May 19;38(6):2660-2672. doi: 10.1093/molbev/msab037. PMID: 33547786; PMCID: PMC8136496.

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.