Quickstart

Set up your analysis

To customize the behavior of the pipeline to fit your needs you can edit the config.yaml file in the data/ folder.

  1. Make a copy of the config.yaml.template file:

$ cp data/config.yaml.template data/config.yaml

  1. In your new config.yaml files you need to enter the correct name for the data.csv containing the species which should be included in the tree:

species: data/data.csv

  1. Also you need to specify the correct BUSCO set and augustus species:

busco:
        set: fungi_odb9
        ausgustus_species: anidulans

You will also need to provide a list of genomes which should be used in your analysis. To do this, edit your data.csv file

The data.csv file should look something like this:

$ cat data.csv
species,Organism_Groups,Size(Mb),Chromosomes,Organelles,Plasmids,Assemblies,web_local
"Ascobolus_immersus","Eukaryota;Fungi;Ascomycetes",59.5299,0,0,0,1,web
"Ascodesmis_nigricans","Eukaryota;Fungi;Ascomycetes",27.3852,0,0,0,1,web
"Cerataphis_brasiliensis_yeast-like_symbiont","Eukaryota;Fungi;Ascomycetes",25.4655,0,0,0,1,web
"Choiromyces_venosus","Eukaryota;Fungi;Ascomycetes",126.035,0,0,0,1,web
"Endocalyx_cinctus","Eukaryota;Fungi;Ascomycetes",44.7739,0,0,0,1,web
"Margaritispora_aquatica","Eukaryota;Fungi;Ascomycetes",42.5173,0,0,0,1,web
"Morchella_conica","Eukaryota;Fungi;Ascomycetes",52.4255,0,0,0,2,web
"Neolecta_irregularis","Eukaryota;Fungi;Ascomycetes",14.1826,0,0,0,1,web
"Nilaparvata_lugens_yeast-like_symbiont","Eukaryota;Fungi;Ascomycetes",26.8096,0,0,0,1,web
"Pneumocystis_carinii","Eukaryota;Fungi;Ascomycetes",7.66146,0,0,0,1,web
"Pneumocystis_jirovecii","Eukaryota;Fungi;Ascomycetes",8.39624,0,0,0,3,web
"Protomyces_sp._C29","Eukaryota;Fungi;Ascomycetes",11.928,0,0,0,1,web
"Sclerotium_cepivorum","Eukaryota;Fungi;Ascomycetes",56.335,0,0,0,1,web
"Taxomyces_andreanae","Eukaryota;Fungi;Ascomycetes",43.1525,0,0,0,1,web
"Terfezia_boudieri","Eukaryota;Fungi;Ascomycetes",63.2346,0,0,0,1,web
"Amphirosellinia_nigrospora","Eukaryota;Fungi;Ascomycetes",48.1778,0,0,0,1,data/assemblies/assembly.fas

The basis of this file can be a CSV file directly downloaded from the NCBI Genome Browser . Just mind the changed header and additional column in the example above. The mandatory columns are the species and the web_local column. The first is the species name and the second specifies whether the genome is provided locally (in which case you should specify the path to the assembly) or not (in which case you should specify web). It is important that the species names correspond exactly to the names under which a genome is deposited at NCBI. Therefore it makes sense to use a downloaded file from the NCBI Genome Browser and add local species to them. However, you can also run the pipeline with only your own assemblies without downloading anything.

It is possible to be even more specific about which genome should be downloaded from NCBI for each taxon by providing a specific accession number directly in the data.csv file by appending =ACCESSION to the last column:

For example by changing the line:

to

phylociraptor will download the first deposited assembly for Ascobolus immersus (GCA_003788565.1) instead of the most recent assembly (GCA_003788565.2).

Running phylociraptor

A typical run of phylociraptor would look like this:

Note

These example commands here assume phylociraptor is run on an SGE cluster. Keep in mind that the provide cluster config files will need to be adjusted to fit your cluster configuration.

1. Setup the pipeline:

Before phylociraptor can be run it is usually a good idea to make copies of the cluster configuration template files before setup is run. Typically the cluster config files will need to be adjusted slightly to fit the configuration of your HPC system.

$ cp data/cluster-config-SGE.yaml.template data/cluster-config-SGE.yaml
$ ./phylociraptor setup -t sge -c data/cluster-config.yaml

During this step, phylociraptor will download and organize all necessary input data. This includes downloading genome assemblies for NCBI (if there are any), downloading the BUSCO set specified in the config.yaml file.

2. Infer and filter orthologous genes for all the genomes:

$ ./phylociraptor orthology --cluster sge --cluster-config data/cluster-config-SGE.yaml
$ ./phylociraptor filter-orthology --cluster sge --cluster-config data/cluster-config-SGE.yaml

Note

If you don’t specify a cluster configuration file, phylociraptor will try to use the default files, which (most likely) will not work on your cluster.

3. Create alignments:

$ ./phylociraptor align -t sge -c data/cluster-config-SGE.yaml

4. Trim and filter alignments:

$./phylciraptor filter-align -t sge -c data/cluster-config-SGE.yaml

Optionally you can run extensive model testing for individual alignments. This is done using iqtree. In case you run this step, the next step will use these models. Otherwise phylociraptor will use models specified in the config file.

$ ./phylociraptor model -t sge -c data/cluster-config-SGE.yaml

5. Reconstruct a phylogeny:

$ ./phylociraptor mltree -t sge -c data/cluster-config-SGE.yaml
$ ./phylociraptor njtree -t sge -c data/cluster-config-SGE.yaml
$ ./phylociraptor speciestree -t sge -c data/cluster-config-SGE.yaml

6. Create a report of the run:

$ ./phylociraptor report

Note

You can create a report after each step and then decide how to set parameters for the next step based on the results.

After this step, your results directory should look like this:

$ ls results/
alignments  assemblies  checkpoints  downloaded_genomes  modeltest  orthology  phylogeny  report.html  statistics