NQuire 2016

Introduction

nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on the basis of frequency distributions at variant sites where only two bases are segregating.

For more background see also the publication at BMC Bioinformatics.

Installed version(s)

This version is installed and currently available on environment hpc-env/8.3:

• nQuire/2018.04-GCCcore-8.3.0

Loading / Using NiBabel

To load the desired version of the module, use the command, e.g.

module load hpc-env/8.3
module load nQuire/2018.04-GCCcore-8.3.0

Always remember: this command is case sensitive!

To run nQuire you can simply type

nQuire [command] [options]

for example

nQuire create -b input.bam -o base

A list of commands can be obtained with

nQuire

and available options are shown be

nQuire [command]

More help and some examples are available from the Github page.

Documentation

The full documentation can be found here.