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Virus Mapping

Summary

Search nucleotide reads/contigs against virus reference databases.

Description

Input can be FASTA/FASTQ or an existing MMseqs2 database. The command converts sequence inputs to MMseqs2 format as needed and runs searches against built-in viral databases (RVMT, NCBI_Ribovirus, or all) or a user-supplied target via --db other --db-path.

Usage

rolypoly virus-mapping [OPTIONS]

Options

  • -t, --threads: Threads (all) [1] (type: INTEGER; default: 1)
  • -M, --memory: MEMORY in gb (more) [6] (type: TEXT; default: 6g)
  • -o, --output: output file location - set suffix to .tab, .sam or html [default: .tab] (type: TEXT; default: /clusterfs/jgi/scratch/science/metagen/neri/code/rolypoly_RP_mapping)
  • --keep-tmp: Keep temporary files (type: BOOLEAN; default: False)
  • --db: Select the database to search against. (type: CHOICE; default: all)
  • --db-path: Path to the user-supplied source (required if --db is 'other'). Either a fasta or a path to formatted MMseqs2 virus database (type: TEXT; default: ``)
  • -g, --log-file: Abs path to logfile (type: TEXT; default: /clusterfs/jgi/scratch/science/metagen/neri/code/rolypoly/search_viruses_logfile.txt)
  • -i, --input: Input path to nucl fasta file OR preformatted mmseqs db (type: TEXT; required; default: Sentinel.UNSET)