orfmatch

Transfer feature annotations from a reference genome to a de novo assembled one, where the new genome sequence is from the same or a closely related strain.

Installation

Install using pip:

pip install orfmatch

or from github:

pip install git+https://github.com/mcgilmore/orfmatch.git

Usage

• Input is an assembly in *.fasta format, output is a are in GenBank format (*.gbff).
• Reference file can be a genome in GenBank format (*.gbff) or a fasta file containing protein sequences (*.fasta or *.faa).

orfmatch --input <assembly.fasta> --reference <reference.gbff/.fasta> --output <output.gbff>

Optional

• -e / --e-value: E value cutoff for phmmer protein match search (default: 1e-25).
• -v / --variants: Outputs matched sequences with differences from the reference to variants.fasta and alignment to variants_alignment.txt.
• -c / --circle: Produces a circle plot with features mapped between reference and assembly in SVG format.
• -l / --line: Produces a linear plot with features mapped between reference and assembly in SVG format.
• -t / --threads: Number of threads used for processing (default: 8)