Fast Plant Plastid Annotation

We can use a set of known genes to annotate a plant plastid genome. The gene set differs slightly between clades of land plant. These genes have been taken from public databases (NCBI), and turned into a set of HMM profiles for each clade of plant (currently supported are Liverworts, Hornworts, Mosses, Ferns, Conifers, and flowering plants). These can then be quickly queried against a genome, without the need for a reference.

Usage

In order to use fppa you will need two things. First you will need to get a binary of the executable fppa.

# assuming you have rust, if not - https://www.rust-lang.org/
git clone https://github.com/tolkit/fppa/
cd fppa
# install to PATH
cargo install --path=.
# bring up the help
fppa -h

# or install to ./target/release
cargo build --release
# bring up the help
./target/release/fppa -h

<Max Brown; Wellcome Sanger 2022>
Fast plant mito annotation (fppa).
Version: 0.1.0

USAGE:
  fppa --plant-chloro <PATH> --nhmmer-path <PATH> --hmms-path <PATH>
FLAGS:
  -h, --help            Prints help information
  -v, --version         Prints version information
ARGS:
  --plant-chloro        Path to the plant chloroplast/plastid genome
  --nhmmer-path         Path to the nhmmer executable (HMMER3)
  --hmms-path           Path to the directory containing a set of
                        HMM files. Download from:
                        https://github.com/tolkit/fppa/tree/main/hmms
OPTIONAL ARGS:
  --plot                Generate an HTML SVG of where the annotated
                        genes occur. Requires a name ending in `.html`.
  --e-value             The E-value cut-off determining presence of
                        mito gene. <default 0.001>
  --gff                 Output a GFF3 file of gene locations. Requires
                        a name ending in `.gff`.
  -r, --for-rotation    Identify only psbA and ycf1 for chloroplast
                        standardisation.

EXAMPLE:
  fppa --plant-chloro ./chloro.fasta --nhmmer-path ./nhmmer --hmms-path ./hmms/angiosperm_hmms/

Secondly you will need a copy of the HMMs for each plant clade. If you git clone'd this repository, they are under the ./hmms directory. You can of course make your own HMMs, but the names will need to match the ones in the hmms directory, otherwise fppa will complain.

An example command:

# the executable
fppa \
# point to the chloroplast genome
--plant-chloro ./genomes/daBalNigr1_segs.fasta \
# point to the nhmmer executable
--nhmmer-path ~/bin/nhmmer \
# point to the directory containing the HMMs (here we're interested in flowering plants)
--hmms-path ./hmms/Magnoliopsida/ \
# generate an HTML SVG of the annotated genes
--plot test.html \
# output a GFF3 file of gene locations
--gff test.gff \
# make a more stringent E value cut-off
--e-value 0.00000001

Output

Output depends on your options. By default a TSV will be printed to STDOUT which shows the presence/absence of each gene in the genome. It's possible to add --plot to generate an HTML file of the annotated genes, and with the --gff option a GFF3 file will be generated.

Reqiurements

You will need the latest version of HMMER, either in your PATH, or you can point fppa to the binary.

Disclaimer

This annotator is not supposed to be extremely complete nor accurate. The aim is just to determine the presence/absence of genes which should be present on a plant chloroplast speedily and without hassle.