Skip to content

Latest commit

 

History

History
82 lines (57 loc) · 3.21 KB

README.md

File metadata and controls

82 lines (57 loc) · 3.21 KB
Raw

parallel-virfinder

Test-Package License Bioconda downloads Bioconda platforms

Run virfinder in parallel, saving both scores and FASTA file

Installation

Via conda:

conda install -c bioconda -c conda-forge parallel-virfinder

Usage

parallel-virfinder.py -i input.fasta -o output.csv -t THREADS [-f output.fasta]

Options

usage: parallel-virfinder.py [-h] -i INPUT -o OUTPUT [-f FASTA] [-n PARALLEL] [-t TMPDIR] [-s MIN_SCORE] [-p MAX_P_VALUE] [--no-check] [-v] [-d]

Execute virfinder on a FASTA file in parallel

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input FASTA file
  -o OUTPUT, --output OUTPUT
                        Output CSV file
  -f FASTA, --fasta FASTA
                        Save FASTA file
  -n PARALLEL, --parallel PARALLEL
                        Number of parallel processes [default: 4]
  -t TMPDIR, --tmpdir TMPDIR
                        Temporary directory [default: /tmp]

VirFinder options:
  -s MIN_SCORE, --min-score MIN_SCORE
                        Minimum score [default: 0.9]
  -p MAX_P_VALUE, --max-p-value MAX_P_VALUE
                        Maximum p-value [default: 0.05]

Running options:
  --no-check            Do not check dependencies at startup
  -v, --verbose         Verbose output
  -d, --debug           Debug output and do not remove temporary files

Test

Clone this repository, activate the conda environment and run:

# Activate the appropriate conda environment, if needed
bash test/test.sh

Benchmark

If compared with a parallel implementation in R, this wrapper performs better (smaller times, smaller memroy usage). See benchmark.

Citations

If you use parallel-virfinder, please cite the following paper:

  • Ren, J., Ahlgren, N. A., Lu, Y. Y., Fuhrman, J. A., & Sun, F. (2017). VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome, 5(1), 1-20.

  • Telatin, A., Fariselli, P., & Birolo, G. (2021). Seqfu: a suite of utilities for the robust and reproducible manipulation of sequence files. Bioengineering, 8(5), 59.

License

VirFinder (see license) is free to use for academic or non commercial use only. SeqFu and this wrapper are free to use.