Disclaimer

This software is not by any means production ready. It has been tested on the Saga compute cluster and on MacOS Sierra. It may break in spectacular ways without any warning. The author appreciates reports of successes and failures, but may not have the capacity to assist with figuring out failures.

Prerequisites

The following software is needed to run the Talos pipeline:

• Java 8 (necessary for Nextflow.io)
• Nextflow.io (obtain from here: Nextflow getting started)
• Illumina sequencing adapters that are needed for Trimmomatic. (can be downloaded from the trimmomatic repo)
• Kraken2 database. ( a minikraken2 database can be downloaded from here: ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/). Instructions for building a complete kraken2 database are found in the kraken2 manual

Download this software.

To install this software simply clone this repository or download the zip archive

Software tools inside Talos

Software that the pipeline uses is installed automatically using conda inside the workflow using the script: 00_set_up_environments.nf. See the running page for instructions on how to run the script

Fastqc version 0.11.8
Multiqc version 1.6
Trimmomatic version 0.39
BBMap version 38.73
Non-Pareil 3 version 3.3.3
Microbcencus version 1.1.1
R-statistics version 3.6.1
Hulk version 1.0.0
Kraken version 2

Note: the software will be installed inside the work directory, which is specified in the nextflow.config file, in a folder called conda. Once installed, it only needs to be installed when the work directory is deleted or cleaned.