HVR Locator

HVR Locator is a workflow to identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR). It aligns query sequences to a reference E. coli full-length 16S rRNA gene and identifies the spanning region through alignment.

Using Singularity to run HVRlocator (Recommended)

1. Download the singularity image (hvrlocator.sif) to your local folder from the following location: Go to https://cloud.sylabs.io/library/jsaraiva/hvrlibrary/hvrlocator

Usage

HVRegLocator can process both SRA accession numbers and FASTA files containing ASV sequences. For specific help on each function type one of the following:

singularity exec hvrlocator.sif hvrlocator sra --help singularity exec hvrlocator.sif hvrlocator align --help

Processing SRA Accession Numbers

To process an SRA run:

singularity exec hvrlocator.sif hvrlocator sra -r SRR1585194 -o /path/to/output/folder

You can specify the location of the E. coli reference file if it's not in the default location:

singularity exec hvrlocator.sif hvrlocator sra -r SRR1585194 --ecoli /path/to/ecoli.fa -o /path/to/output/folder

To process a list of SRA runs:

singularity exec hvrlocator.sif hvrlocator sra -l /path/to/list.txt -o /path/to/output/folder

You can specify the location of the E. coli reference file if it's not in the default location:

singularity exec hvrlocator.sif hvrlocator sra -l /path/to/list.txt --ecoli /path/to/ecoli.fa -o /path/to/output/folder

Note: The list of SRA runs should be 1 per line.

Processing ASV FASTA Files

To process a FASTA file containing ASV sequences:

hvreglocator fasta -f path/to/your/asv_sequences.fasta --ecoli /path/to/ecoli.fa -o /path/to/output/folder

Local Installation (Alternative)

To install HVR Locator locally, follow these steps:

1. Create a new conda environment:

mamba create --prefix /global/apps/hvreglocator/0.2 -y -c bioconda python=3.9 sra-tools mafft fastp biopython numpy scipy vsearch

2. Activate the environment, clone the repository, and install the package:

source activate /global/apps/hvreglocator/0.2 && \
cd /global/apps/hvreglocator/0.2 && \
git clone https://github.com/joao1980/hvrlocator.git && \
cd hvrlocator && \
pip install -e .

Note: Replace the GitHub URL with the appropriate URL for your repository.

Usage

HVRegLocator can process both SRA accession numbers and FASTA files containing ASV sequences.

Processing SRA Accession Numbers

To process an SRA run:

hvreglocator sra -r SRR1585194

You can specify the location of the E. coli reference file if it's not in the default location:

hvreglocator sra -r SRR1585194 --ecoli /path/to/ecoli.fa

Processing ASV FASTA Files

To process a FASTA file containing ASV sequences:

hvreglocator fasta -f path/to/your/asv_sequences.fasta

Output

The script will output the alignment start and end positions, as well as the identified hypervariable region span (e.g., V1-V3).

Project Structure

• hvreglocator.py: The main script that handles both SRA and FASTA processing.
• setup.py: Used for installing the package.

Troubleshooting

If you encounter any issues with finding the E. coli reference file, make sure it's in the same directory as the hvreglocator.py script, or use the --ecoli argument to specify its location.

Contributing

Contributions to HVRegLocator are welcome. Please feel free to submit a Pull Request.

License

This project is licensed under the terms of the MIT license.