README

This is the repository for mytax, a tool for building custom taxonomies, which can aid nucleotide sequence classification.

Installation

Clone this repo with:

git clone https://github.com/tmehoke/mytax

Symbolically link all shell scripts into your path, for example with:

find mytax/src -name "*.sh" | while read fn; do sudo ln -s $PWD/$fn /usr/local/bin; done

Dependencies

• jellyfish (version 1) - https://www.cbcb.umd.edu/software/jellyfish/

• kraken (version 1) - https://ccb.jhu.edu/software/kraken/

• gawk - https://www.gnu.org/software/gawk/manual/html_node/Installation.html

• perl

• GNU CoreUtils

• 16 GB of RAM is needed to build the provided influenza kraken database

Usage

Building example

This pipeline is built from a central set of scripts located in the src directory

Build flu-kraken example with:

build_flukraken.sh -k flukraken-$(date +"%F")

The single script build_flukraken.sh functions as an outer wrapper for the influenza classification example using the Kraken classifier published in the mytax paper.

build_flukraken.sh can also be used as a model to build modified pipelines as desired. It is built from four main sub-modules:

	download_IVR.sh -> download references and taxonomy from IVR

	build_IVR_metadata.sh -> build tab-delimited metadata table in format for mytax

	build_taxonomy.sh -> build custom taxonomy from tab-delimited table

	build_krakendb.sh -> add new taxonomic IDs to reference FASTA, build kraken database, post-process database for visualization pipeline

build_krakendb.sh currently references three helper scripts, which also need to be in the PATH:

	fix_references.sh -> adds new taxonomic IDs to reference FASTA

	kraken-build -> builds kraken database

	process_krakendb.sh -> post-processes database for visualization pipeline (not included in this repo yet)

Running the sunburst

To Run the UI run python3 -m http.server 8080 within the sunburst directory and open localhost:8080 on your favorite web browser

License and copyright

Copyright (c) 2019 Thomas Mehoke

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.