WhatsHap¶

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

homepage: https://whatshap.readthedocs.io

Available installations¶

WhatsHap version	Supported CPU targets	Supported GPU targets	EESSI version	Module
2.1	`generic`: `aarch64`, `x86_64` Arm: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace` AMD: `zen2`, `zen3`, `zen4` Intel: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`	(none)	2023.06	`WhatsHap/2.1-foss-2022b`
2.2	`generic`: `aarch64`, `x86_64` Arm: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace` AMD: `zen2`, `zen3`, `zen4` Intel: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`	(none)	2023.06	`WhatsHap/2.2-foss-2023a`

Extensions¶

Overview of extensions included in WhatsHap installations

pulp¶

`pulp` version	WhatsHap modules that include it
2.8.0	`WhatsHap/2.1-foss-2022b`

PuLP¶

`PuLP` version	WhatsHap modules that include it
2.8.0	`WhatsHap/2.2-foss-2023a`

WhatsHap¶

`WhatsHap` version	WhatsHap modules that include it
2.1	`WhatsHap/2.1-foss-2022b`

whatshap¶

`whatshap` version	WhatsHap modules that include it
2.2	`WhatsHap/2.2-foss-2023a`

xopen¶

`xopen` version	WhatsHap modules that include it
1.7.0	`WhatsHap/2.1-foss-2022b` `WhatsHap/2.2-foss-2023a`