HGT detection pipeline v.1

Usage

Add your own (sub)-taxonomy

Insert tutorial

Installation

Dependencies

• snakemake - conda
• hgtector2 - pip
• taxonkit - conda
• blast suite - conda
• mafft - conda
• proteinortho - conda
• famsa - conda
• seqkit - conda
• trimal - conda
• fasttree - conda
• FastRoot - pip
• tidyverse R package - CRAN
• phytools -CRAN
• ggtree - Bioconductor
• ggtreeExtra - Bioconductor
• Biostrings - Bioconductor
• ComplexHeatmap - Bioconductor

You can use conda to create this environment, ideally use mamba:

conda create -c conda-forge -c bioconda -n hgt snakemake
conda activate hgt

# install hgtector
conda install -c conda-forge pyyaml pandas matplotlib scikit-learn bioconda::diamond
pip install git+https://github.com/qiyunlab/HGTector.git

# install other dependencies
conda install -c bioconda mafft trimal fasttree taxonkit proteinortho famsa seqkit

# install R if you need
conda install -c conda-forge r-base
conda install -c conda-forge -c bioconda r-tidyverse r-optparse r-magic r-phytools bioconductor-ggtree bioconductor-ggtreeextra bioconductor-complexheatmap 
bioconductor-biostrings

# install fastroot
python3 -m pip install FastRoot
fr=$(which FastRoot.py)
dos2unix $fr

TODOs

• mask proteins and then do dataframe with protein length, %masked proportion to eventually filter downstream results

• add link to deps

• what to do if less than 2 seqs in plot_Tree?

• more elegant way to get sequences to do the tree

• add QC plots

• what to do with foldseek?

• matreex plots?

• mark HGT tree by topological rule

• get df of tree with all different properties so user can filter

• when deleting hits from the same species you may remove paralogs that are not identified by proteinortho but still may be close in the tree

• annotate domains and protein functions

• maybe one strategy would be to compute big trees in a fast way then reduce taxonomic redundancy and compute a more accurate tree

• remove fastroot dependency

• option to define "close" outgroup and compute other indexes

• identify potential donors from blast results (recurring weird taxons)

• one day 3 modalities

  • --interdomain: easy mode for proka2euka lgt
  • --donors: user-defined putative donors
  • --reconcile: with small curated database and species tree run reconciliation