BuscoPhylo

Pipeline to construct species phylogenies using BUSCOs.

The pipeline automatically creates the directory structure from the config file. Default directory structure:

|-results
    |- busco
    |- ids
    |   |- species_ids
    |   |- common_ids
    |   |- merged_sequences  
    |- alignments
    |   |- raw
    |   |- trimal
    |- concat_alignments
    |- phylogeny
    |   |- iqtree
    |   |- mrbayes

Usage example

snakemake --snakefile Snakemake --profile profile/slurm/ --configfile config/default.yaml \
    --config genome_dir="" busco_dataset_path="" trimal_path="" iqtree_path="" mrbayes_path="" \
    --printshellcmds --latency-wait 60

Requirements

• Snakemake
• BUSCO v3.0.2 or BUSCO v5.2.2
• MAFFT
• PRANK
• TrimAl
• IQ-TREE
• MrBayes

You can select the BUSCO version (v3.0.2 or v5.2.2). To do this, specify the value of busco_version 3 or 5 in config file. You can also choose MAFFT or PRANK to align sequences by specifying 'mafft' or 'prank' in the alignment_tool option in config file. PRANK is only used for DNA sequences! Protein sequences are processed with MAFFT in both cases.

BUSCO v3.0.2, TrimAl, IQ-TREE and MrBayes paths should be in config file or specified at startup. BUSCO v5.2.2, MAFFT and PRANK are installed using a conda.