Tutorial

Basic settings

Commands

GeneSeekr requires the desired BLAST program to be specified. The acceptable options are:

* blastn (nucleotide:nucleotide)
* blastp (protein:protein)
* blastx (translated nucleotide:protein)
* tblastn (protein:translated nucleotide)
* tblastx (translated nucleotide: translated nucleotide)

Arguments

The pipeline is designed to run with a minimum of three arguments:

* path to sequence data (-s)
* path to target database (-t)
* path in which report folder is to be created (-r)

The following command will run geneseekr using BLASTn on the supplied sequences and database

geneseekr blastn -s /path/to/sequences -t /path/to/targets -r /path/to/reports

Optional Arguments

There are a number of optional arguments than can be supplied to the geneseekr script

  Options:
  -s, --sequencepath TEXT   Specify input fasta folder  [required]
  -t, --targetpath TEXT     Specify folder of targets  [required]
  -r, --reportpath TEXT     Specify output folder for csv  [required]
  -c, --cutoff INTEGER      Minumum sequence identity threshold for a match to
                            be reported
  -e, --evalue TEXT         Minimum evalue to use for BLAST analyses
  -n, --numthreads INTEGER  Specify number of threads
  -a, --align               Optionally output alignments of genes with less
                            than 100% identity to reference genes. This
                            alignment will use amino acid sequences for both
                            query and reference
  -u, --unique              Do not report multiple hits at the same location
                            in a contig. Instead, store the best hit, and
                            ignore the rest
  --version                 Show the version and exit.
  -h, --help                Show this message and exit.

Additional Optional Arguments

If you use a BLAST program that employs a nucleotide database(BLASTn, tBLASTn, or tBLASTx) the following arguments are available:

  -R, --resfinder           Perform ResFinder-like analyses
  -V, --virulencefinder     Perform VirulenceFinder-like analyses