add phold to docs

README.md

@@ -1,3 +1,5 @@
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/gbouras13/pharokka/blob/main/run_pharokka_and_phold.ipynb)
+
 [![Paper](https://img.shields.io/badge/paper-Bioinformatics-teal.svg?style=flat-square&maxAge=3600)](https://doi.org/10.1093/bioinformatics/btac776)
 [![CI](https://github.com/gbouras13/pharokka/actions/workflows/ci.yaml/badge.svg)](https://github.com/gbouras13/pharokka/actions/workflows/ci.yaml)
 [![BioConda Install](https://img.shields.io/conda/dn/bioconda/pharokka.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/pharokka)
@@ -23,10 +25,26 @@ Extra special thanks to Ghais Houtak for making Pharokka's logo.
 
 If you are looking for rapid standardised annotation of bacterial genomes, please use [Bakta](https://github.com/oschwengers/bakta). [Prokka](https://github.com/tseemann/prokka), which inspired the creation and naming of `pharokka`, is another good option, but Bakta is [Prokka's worthy successor](https://twitter.com/torstenseemann/status/1565471892840259585).
 
+# phold
+
+If you like `pharokka`, you will probably love [phold](https://github.com/gbouras13/phold). `phold` uses structural homology to improve phage annotation. Benchmarking is ongoing but `phold` strongly outperforms `pharokka` in terms of annotation, particularly for less characterised phages such as those from metagenomic datasets.
+
+`pharokka` still has features `phold` lacks for now (identifying tRNA, tmRNA, CRISPR repeats, and INPHARED taxonomy search), so it it recommended to run `phold` after running `pharokka`. 
+
+`phold` takes the Genbank output of Pharokka as input. Therefore, if you have already annotated your phage(s) with Pharokka, you can easily update the annotation with more functional predictions with [phold](https://github.com/gbouras13/phold).
+
+
+# Google Colab Notebooks
+
+If you don't want to install `pharokka` or `phold` locally, you can run `pharokka` and `phold`, or only `pharokka` it without any code using the Google Colab notebook [https://colab.research.google.com/github/gbouras13/phold/blob/main/run_pharokka_and_phold.ipynb](https://colab.research.google.com/github/gbouras13/phold/blob/main/run_pharokka_and_phold.ipynb)
+
+
 # Table of Contents
 
 - [pharokka](#pharokka)
   - [Fast Phage Annotation Tool](#fast-phage-annotation-tool)
+- [phold](#phold)
+- [Google Colab Notebooks](#google-colab-notebooks)
 - [Table of Contents](#table-of-contents)
 - [Quick Start](#quick-start)
 - [Documentation](#documentation)

docs/index.md

@@ -4,6 +4,18 @@
 
 ![Image](pharokka_logo.png)
 
+# phold
+
+If you like `pharokka`, you will probably love [phold](https://github.com/gbouras13/phold). `phold` uses structural homology to improve phage annotation. Benchmarking is ongoing but `phold` strongly outperforms `pharokka` in terms of annotation, particularly for less characterised phages such as those from metagenomic datasets.
+
+`pharokka` still has features `phold` lacks for now (identifying tRNA, tmRNA, CRISPR repeats, and INPHARED taxonomy search), so it it recommended to run `phold` after running `pharokka`. 
+
+`phold` takes the Genbank output of Pharokka as input. Therefore, if you have already annotated your phage(s) with Pharokka, you can easily update the annotation with more functional predictions with [phold](https://github.com/gbouras13/phold).
+
+# Google Colab Notebooks
+
+If you don't want to install `pharokka` or `phold` locally, you can run `pharokka` and `phold`, or only `pharokka` it without any code using the Google Colab notebook [https://colab.research.google.com/github/gbouras13/phold/blob/main/run_pharokka_and_phold.ipynb](https://colab.research.google.com/github/gbouras13/phold/blob/main/run_pharokka_and_phold.ipynb)
+
 ## Overview
 
 `pharokka` uses [PHANOTATE](https://github.com/deprekate/PHANOTATE), the only gene prediction program tailored to bacteriophages, as the default program for gene prediction. [Prodigal](https://github.com/hyattpd/Prodigal) implemented with [pyrodigal](https://github.com/althonos/pyrodigal) and [Prodigal-gv](https://github.com/apcamargo/prodigal-gv) implemented with [pyrodigal-gv](https://github.com/althonos/pyrodigal-gv) are also available as alternatives. Following this, functional annotations are assigned by matching each predicted coding sequence (CDS) to the [PHROGs](https://phrogs.lmge.uca.fr), [CARD](https://card.mcmaster.ca) and [VFDB](http://www.mgc.ac.cn/VFs/main.htm) databases using [MMseqs2](https://github.com/soedinglab/MMseqs2). As of v1.4.0, `pharokka` will also match each CDS to the PHROGs database using more sensitive Hidden Markov Models using [PyHMMER](https://github.com/althonos/pyhmmer). Pharokka's main output is a GFF file suitable for using in downstream pangenomic pipelines like [Roary](https://sanger-pathogens.github.io/Roary/). `pharokka` also generates a `cds_functions.tsv` file, which includes counts of CDSs, tRNAs, tmRNAs, CRISPRs and functions assigned to CDSs according to the PHROGs database. See the full [usage](#usage) and check out the full [documentation](https://pharokka.readthedocs.io) for more details.