https://github.com/tomarovsky/buscoclade
Snakemake pipeline to construct species phylogenies using BUSCOs
https://github.com/tomarovsky/buscoclade
busco phylogenomics sciworkflows snakemake
Last synced: 2 months ago
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Snakemake pipeline to construct species phylogenies using BUSCOs
- Host: GitHub
- URL: https://github.com/tomarovsky/buscoclade
- Owner: tomarovsky
- License: mit
- Created: 2022-11-14T14:38:57.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2025-11-30T16:31:01.000Z (5 months ago)
- Last Synced: 2025-12-02T21:23:54.163Z (5 months ago)
- Topics: busco, phylogenomics, sciworkflows, snakemake
- Language: Python
- Homepage:
- Size: 463 KB
- Stars: 4
- Watchers: 2
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Snakemake workflow: BuscoClade
[](https://snakemake.github.io)
[](https://opensource.org/licenses/MIT)
## Description
Pipeline to construct species phylogenies using [BUSCO](https://busco.ezlab.org/).
- Alignment: [PRANK](http://wasabiapp.org/software/prank/), [MAFFT](https://mafft.cbrc.jp/alignment/software/).
- Trimming: [GBlocks](https://academic.oup.com/mbe/article/17/4/540/1127654), [TrimAl](http://trimal.cgenomics.org/).
- Phylogenetic tree constraction: [IQTree](http://www.iqtree.org/), [MrBayes](https://nbisweden.github.io/MrBayes/), [ASTRAL-IV](https://doi.org/10.1093/molbev/msaf172), [RapidNJ](https://birc.au.dk/software/rapidnj), [PHYLIP](https://phylipweb.github.io/phylip/), [RAxML-NG](https://github.com/amkozlov/raxml-ng).
- Visualization: [Etetoolkit](http://etetoolkit.org/), [Matplotlib](https://matplotlib.org/stable/).
## Usage
### Step 1. Deploy workflow
To use this workflow, you can either download and extract the [latest release](https://github.com/tomarovsky/BuscoClade/releases) or clone the repository:
```
git clone https://github.com/tomarovsky/BuscoClade.git
```
### Step 2. Add species genomes
Place your FASTA genome assemblies into the `genomes/` directory. Keep in mind that the file prefixes will influence the output phylogeny. The pipeline supports FASTA files with the extensions `.fasta`, `.fna`, and `.fa`, including their gzipped versions (e.g., `.fasta.gz`, `.fna.gz`, `.fa.gz`).
### Step 3. Configure workflow
To set up the workflow, modify `config/default.yaml`. I recommend to copy config gile and do all modifications in this copy. Some of the options (all nonested options from default.yaml) could also be set via command line using `--config` flag. Sections of config file:
- **Pipeline Configuration:**
This section outlines the workflow. By default, it includes alignments and following filtration of nucleotide sequences, and all tools for phylogeny reconstruction, except for MrBayes (it is recommended to run the GPU compiled version separately). To disable a tool, set its value to `False` or comment out the corresponding line.
- **Tool Parameters:**
Specify parameters for each tool. To perform BUSCO, it is important to specify:
- `busco_dataset_path`: Download the BUSCO dataset beforehand and specify its path here.
- `busco_params`: Use the `--offline` flag and the `--download_path` parameter, indicating the path to the `busco_downloads/` directory.
- **Directory structure:**
Define output file structure in the `results/` directory. It is recommended to leave it unchanged.
- **Resources:**
Specify Slurm queue, threads, memory, and runtime for each tool.
### Step 4. Execute workflow
Install snakemake:
```
mamba create -c conda-forge -c bioconda -c nodefaults -n snakemake snakemake snakemake-executor-plugin-cluster-generic
mamba activate snakemake
```
For a dry run:
```
snakemake --profile profile/slurm/ --configfile config/default.yaml --dry-run
```
Snakemake will print all the rules that will be executed. Remove `--dry-run` to initiate the actual run.
**How to run the workflow if I have completed BUSCOs?**
First, move the genome assemblies to the `genomes/` directory or create empty files with corresponding names. Then, create a `results/busco/` directory and move the BUSCO output directories into it. Note that BUSCO output must be formatted. Thus, for `Ailurus_fulgens.fasta` BUSCO output should look like this:
```
results/
busco/
Ailurus_fulgens/
busco_sequences/
fragmented_busco_sequences/
multi_copy_busco_sequences/
single_copy_busco_sequences/
hmmer_output/
logs/
metaeuk_output/
full_table_Ailurus_fulgens.tsv
missing_busco_list_Ailurus_fulgens.tsv
short_summary_Ailurus_fulgens.txt
short_summary.json
short_summary.specific.mammalia_odb10.Ailurus_fulgens.json
short_summary.specific.mammalia_odb10.Ailurus_fulgens.txt
```
## Contact
Please email me at: for any questions or feedback.