orfmatch 0.1.1

Transfer feature annotations from a reference genome to a de novo assembled one.

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

orfmatch [-v (Optional: outputs sequence variants as fasta and alignments)] --input <assembly.fasta> --reference <reference.gbff> --output <output.gbff>

• Input is an assembly in *.fasta format.
• Reference genome and output genome are in GenBank format (*.gbff).
• Optionally, sequences which differ from the reference but are still classified as the same by pyhmmer can be output using the -v or --variants argument. A fasta file containing all varying sequences and pairwise alignments will be output to variants.fasta and variants_alignment.txt respectively.