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
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
git clone https://github.com/talnor/TIME_pipeline.git
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.
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.
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>
- Ensure the settings in the
nextflow.configare 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.
Check the command help for more info and options.
nextflow run main.nf --help
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>