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Determining time of infection for human immunodeficiency viruses

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TIME_pipeline

Determining time of infection for human immunodeficiency viruses.

The analysis builds upon the Shiver tool for mapping paired-end short reads to a custom reference sequence constructed using do novo assembled contigs. Base frequencies from the alignment are then used to calculate the time of infection based on the accumulated mutations in the pol gene as described in the publication by Puller et al.

Neher R, Albert J (2017), Estimating time of HIV-1 infection from next-generation sequence diversity. PLoS Comput Biol 13(10): e1005775. https://doi.org/10.1371/journal.pcbi.1005775

Installation and set up

Install required software

Make sure the following is installed, or install them:

  • Singularity or Docker
  • Nextflow or conda (install nextflow using conda as described below)
conda create -n time_analysis nextflow
conda activate time_analysis

Install TIME_pipeline

git clone https://github.com/talnor/TIME_pipeline.git

Configure pipeline options in the nextflow config file

Default parameters and settings for running the pipeline are specified in nextflow.config. Important settings to change include:

Settings Description
hostGenome Directory with human reference genome database (bwa)
hostGenomeBase The name (base) of the database files
cache Directory for cache files
process.clusterOptions Cluster options if using slurm for execution

In addition, default settings for primers, adapters and similar configurations are described in more detail here.

Download host reference genome

For example, the following command can be run to download the human reference genome:

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz

Then set up the host database with the following command. The database will be placed in the hostGenome directory and will be namned as hostGenomeBase.

nextflow run main.nf --setup -profile slurm,singularity --hostFasta <path_to_genome> --outdir <outdir>

To run this pipeline in Bianca, the project-id must be defined in the clusterOptions.

Run Shiver initialisation

The Shiver initialization directory includes the set of primers used during the amplification of the samples as well as a reference dataset to be used in the analysis. Several options are included in this repository. Information on these are available here. To create your own initialization directory, run the following command:

nextflow run main.nf --init -profile slurm,singularity --primers <primers.fasta> --adapters <adapters.fasta> --config <shiver_config.sh> --references <references.fasta> --outdir <outdir>

Usage

  • Ensure the settings in the nextflow.config are correct for your samples. Importantly, the primer set and the initialization directory needs to match the primers used during amplification of the samples. Or override the default values by supplying them as parameters in the command below.

Basic usage:

conda activate time_analysis
nextflow run main.nf -profile slurm,singularity --input 'path/to/*_R{1,2}.fastq.gz' --outdir path/to/results/ --ticket <batch_name>

The pipeline can be executed on your local computer or with a slurm resource manager. The container can be run using docker or singularity. The above command would run the pipeline using slurm and singularity.

Options

Check the command help for more info and options.

nextflow run main.nf --help

Optional installation steps

Set up container image

A container image is available from Docker at talnor/hiv_time_analysis. By default, this image will be used when using the docker or singularity profiles. If this doesn't work, the container can be manually downloaded, or rebuilt from the Dockerfile in this repo. If so update the settings in the nextflow.config.

  • manually pull singularity image: singularity pull path/to/hiv_time_analysis.sif docker://talnor/hiv_time_analysis:<version>
  • manually pull docker image: docker pull talnor/hiv_time_analysis:<version>

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