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virus_pipe

virus_pipe is a command-line workflow for virus discovery from sequencing data.

It supports input files in:

  • *.fastq
  • *.fastq.gz
  • *.fasta

The pipeline orchestrates trimming, QC, assembly, mapping, unmapped read extraction, contig construction, blastn/blastx, and virus-focused discovery.

Repository contents

  • virus_pipe.sh – main analysis pipeline.
  • build_dictionary.sh – helper script to build a BWA/Picard/SAMtools reference index.
  • virus_database.py – adds ICTV/NCBI taxonomy information to candidate virus hits.
  • reverse.py – helper used while generating adapter sequences.
  • ICTV_corrected.txt, ICTV_and_NCBI_Tax.txt – taxonomy lookup tables used by virus_database.py.

Requirements

The scripts assume these tools are available in your environment/path (or at the hard-coded locations in the scripts):

  • Java
  • Trimmomatic
  • FastQC
  • Trinity
  • BWA
  • SAMtools
  • Picard
  • CAP3
  • BLAST+ (blastn, blastx)
  • fasta_formatter
  • Python (for virus_database.py and reverse.py)

Note: virus_pipe.sh currently contains cluster-specific absolute paths (for example /local/cluster/...). Update those paths for your environment.

1) Build a reference dictionary

Before running the main pipeline, build a reference dictionary from a FASTA reference:

./build_dictionary.sh reference.fasta

This creates a directory named after reference with BWA, Picard dictionary (.dict), and samtools faidx outputs.

2) Configure virus_pipe.sh

In virus_pipe.sh, update the dictionary selection block to point to your reference index path.

Current logic expects a key and path placeholder:

if [ $2 = "genome_to_map_to" ]; then
    Dictionary="location"
fi

Replace:

  • genome_to_map_to with the key you want to pass as the second argument.
  • location with the actual reference index prefix path.

3) Run the pipeline

./virus_pipe.sh your_file.fastq genome_to_map_to

Where:

  • your_file.fastq can also be *.fastq.gz or *.fasta.
  • genome_to_map_to is the dictionary key configured in the script.

The script creates an output folder named after the input basename and writes intermediate files, BLAST reports, and a final *_virus_report.txt summary.

Notes

  • The default resource settings in virus_pipe.sh are:
    • CPU=8
    • memory=64G
  • Intermediate files are compressed during processing to reduce disk usage.
  • Legacy mention of crawler.sh has been removed from this README because that script is not present in this repository.