Installation

A Makefile is provided to create a virtual environment into which katuali will be installed.

Katuali has been tested on Linux (specifically Ubuntu 16) and MacOS.

To setup the environment run:

git clone https://github.com/nanoporetech/katuali.git
cd katuali
make install
source ./venv/bin/activate

Dependencies

Katuali makes use of a number of tools to perform basecalling, assembly, and polishing that need to be installed in order to perform such steps of a pipeline. Katuali does not enforce that all possible tools are present; only those required to run a user’s pipeline need be installed. If Katuali cannot find a tool, it will alert the user.

The list below indicates possible options for pipeline steps and the default filesystem location where Katuali expects to find them. Each item is shown as must be specified in the pipeline configuration, the locations can be changed by the user as appropriate.

Refer to the documentation of each of these tools for installation instructions.

General Tools

pomoxis: "~/git/pomoxis/venv/bin/activate"

Pomoxis is used as a general utility throughout much of katuali, its installation is required for most functionality.

Pomoxis >= 0.3.2 is required for the medaka variant-calling training pipelines.

Basecalling Tools

guppy: "/usr/bin/guppy_basecaller"

Assembly Tools

canu: "~/git/canu-1.8/Linux-amd64/bin/canu"
flye: "~/git/Flye/bin/flye"
shasta: "~/git/shasta-Linux-0.3.0"
pomoxis: "~/git/pomoxis/venv/bin/activate"

In the context of Katuali, pomoxis functions as a wrapper to miniasm. Canu is utilised in the standard workflow, while pomoxis is used in the fast workflow.

Consensus Tools

medaka: "~/git/medaka/venv/bin/activate"

Note

Note that tensorflow-gpu must be installed in your medaka environment if you wish to run medaka using a GPU (required for medaka training, optional for running medaka consensus)

Katuali can also use racon which is included with pomoxis.

Other tools

liftover: "~/miniconda3/envs/liftover/bin/liftOver"
vcfcreatemulti: "~/git/vcflib/bin/vcfcreatemulti"

LiftOver and vcfcreatemulti are used in the medaka variant-calling training pipelines and only needs to be installed if you intend to use these pipelines.