twelvesummer/uvp

Mycobacterium tuberculosis next generation sequence analysis

UVP

Set of scripts for analyzing NGS data

Software dependencies:

Name	Version
bedtools	2.17.0
bcftools	1.2
bwa	0.7.12
fastqc	0.11.5
fqtools	2.0
gatk	3.6
kraken	0.10.5
picard	1.141
prinseq	0.20.4
pigz	2.3.4
qualimap	2.1.3
samtools	1.2
snpeff	4.1
perl-vcftools-vcf	0.1.16
vcftools	0.1.16

Installation

The UVP requires at least 100GB RAM and up to 100GB storage space to run locally. Insatlling the UVP on your local machine is straight forward. Clone the entire repository, then create a conda environment using the environment.yml file provided:

conda env create -f environment.yml

Then activate the environment:

conda activate reseqtb-uvp

With the reseqtb-uvp conda environment active, run the following command from withing the top-level directory of the 'UVP' repository to install the UVP code into the conda environment:

pip install -e .

Note: the -e flag installs UVP in 'editable' mode so that any changes to the code-base will be automatically installed into the conda environment.

Due to the terms of the GATK v3 license, it will be necessary to download and install the GATK .jar file separately. Download the GATK .tar.bz2 file from this link:

https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.6-0-g89b7209

...then decompress it:

tar -xjvf GenomeAnalysisTK-3.6-0-g89b7209.tar.bz2 

...and (with the reseqtb-uvp conda environment active) register the GenomeAnalysisTK.jar file:

gatk-register GenomeAnalysisTK.jar

The GenomeAnalysisTK.jar file will be copied into the appropriate directory inside your reseqtb-uvp conda environment.

Download the M. tuberculosis H37Rv snpEff database

A M. tuberculosis snpEff database is necessary for annotating variants. With the reseqtb-uvp conda environment active, run the following command to download it:

snpEff download m_tuberculosis_H37Rv

Configuration

The following configuration settings may be supplied in a configuration file instead of providing them as command-line arguments:

• Path to kraken database
• Number of CPU threads for parallel execution

The config file should be a valid yaml file with this structure:

directories:
    krakendb: /data/ref_databases/kraken/minikraken
other:
    threads: 8

When UVP is installed, a config.yml file is stored in lib/python<version>/site-packages/uvp/config.yml. The user may edit that file to provide the appropriate configuration settings. Alternatively, a config.yml can be provided using the -c or --config flags when an analysis in initiated. A config file supplied using the -c or --config flag will override any settings stored in the installed config file.

The krakendb and threads parameters can also be supplied directly using the -k/--krakendb and -t/--threads flags, respectively. If those flags are included when starting an analysis they will override any values in config files.

Running the UVP

Run the UVP using command line prompts as follows:

uvp \
  -n 'sample name' \
  -r 'path to H37Rv reference genome fasta file' \
  -q 'input fastq' \
  -q2 'paired fastq file' \
  --annotate \
  --verbose 

When passing a config file, use the -c or --config flag:

uvp \
  -c 'path to config file' \
  -n 'sample name' \
  -r 'path to H37Rv reference genome fasta file' \
  -q 'input fastq' \
  -q2 'paired fastq file' \
  --annotate \
  --verbose 

...or set the krakendb and threads parameters directly on the command-line:

uvp \
  -n 'sample name' \
  -r 'path to H37Rv reference genome fasta file' \
  -q 'input fastq' \
  -q2 'paired fastq file' \
  --krakendb 'path to kraken database' \
  --threads 16 \
  --annotate \
  --verbose