BUSCO to Phylogeny Pipeline

This pipeline is modified from by Magnus Wolf 2021 (magnus.wolf@senckenberg.de). It can be used to running BUSCO program and generate the supermatrix/supertree automatically.

Installation

This pipeline can be easily installed from conda and use via simple configuration

Downloading the main pipeline

wget https://github.com/mag-wolf/BUSCO-to-Phylogeny/blob/main/BUSCO-to-Phylogeny.tar.gz
tar BUSCO-to-Phylogeny.tar.gz BUSCO-to-Phylogeny
cd BUSCO-to-Phylogeny
unzip *.zip

Install all the dependency via different conda enviroment

conda create --name MAFFTenv
conda install -n MAFFTenv -c bioconda mafft
conda create --name CLIPKITenv
conda install -n CLIPKITenv -c jlsteenwyk clipkit
conda create --name IQTREEenv
conda install -n IQTREEenv -c bioconda iqtree
conda create --name BUSCOenv
conda install -n BUSCOenv -c bioconda -c conda-forge busco =5.3.2

Configuration

1.) Gather whole genome assemblies in fasta format for all species you want to have in your tree. Copy them to the work directory and rename as the species name accordingly.

2.) Open the script BUSCO-to-Phylogeny.sh with a text editor and change the dependencies and working directory as you have. Make sure the conda environment are correct.

3.) Edit BUSCO-to-Phylogeny dependencies and parameters. Especially the OrthoDB database for BUSCO and the augustus training species you want to use.

4.) Edit options for BUSCO-to-PHYLOGENY. Call everything “TRUE” that you want to use. The pipeline contains 10 subparts that can be run independently if all other subparts are called “FALSE”. By leaving it as it is, everything will run one by one.

5.) Delete the config.ini in your working directory unless you want to set the BUSCO by yourself.

6.) Now simply run: Reads assembly are using long reads as skeleton and short reads for correction.

bash BUSCO-to-Phylogeny.sh 2>&1 | tee error.log

List of all subparts for pipeline and canbe run individually

runbusco                   #run the BUSCO tool on every assembly for annotation and getting single copy orthologs.
findsharedscos             #find BUSCO genes that are shared between all of the species you provided
makealignments             #make alignments of all gene sequences using mafft
trimmgenealignments        #trimm the alignments using clipkit
filteralignments           #filter the alignments for to conserved genes
concatgenealignments       #concatenate gene alignments into one big matrix using FASconCAT
trimmsupermatrix           #trimm the concatenated alignment using clipkit
constructgenetrees         #constructing gene trees of every single gene alignment using iqtree
constructsupermtree        #constructing a tree from the concatenated alignment using iqtree
constructsuperttree        #constructing a consensus tree based on all constructed genes trees using Astral

Other BUSCO to Phylogeny method

BuscoOrthoPhylo		https://github.com/PlantDr430/BuscoOrthoPhylo
BUSCOfilter			https://github.com/Rowena-h/BUSCOfilter
BUSCO_Phylogenomics	https://github.com/jamiemcg/BUSCO_phylogenomics
busco_tree			https://github.com/zengxiaofei/busco-tree
busco2phylo-nf		https://github.com/lstevens17/busco2phylo-nf