SuperPang 1.1.0.post3

Non-redundant pangenome assemblies from multiple genomes or bins

SuperPang: non-redundant pangenome assemblies from multiple genomes or bins

Check our paper: Puente-Sánchez F, Hoetzinger M, Buck M and Bertilsson S. Exploring intra-species diversity through non-redundant pangenome assemblies Molecular Ecology Resources (2023) DOI: 10.1111/1755-0998.13826

... but note that performance is now better (3x less memory usage, 20% faster execution time) than when we first benchmarked Superpang.

Installation

Requires graph-tool, speedict, mOTUlizer v0.2.4, minimap2 and mappy. The easiest way to get it running is using conda.

# Install into a new conda environment
conda create -n SuperPang -c conda-forge -c bioconda -c fpusan superpang
# Check that it works for you!
conda activate SuperPang
test-SuperPang.py

Usage

SuperPang.py --fasta <genome1.fasta> <genome2.fasta> <genomeN.fasta> --checkm <check_results> --output-dir <output_directory>

Input files and choice of parameters

• The input genomes can be genomes from isolates, MAGs (Metagenome-Assembled Genomes) or SAGs (Single-cell Assembled Genomes).
• The input genomes can have different qualities, for normal usage we recommend that you provide completeness estimates for each input genome through the -q/--checkm parameter.
• If you are certain that all your input genomes are complete, you can use the --assume-complete flag or manually tweak the -a/--genome-assignment-threshold and -x/--default-completeness parameters instead of providing a file with completeness estimates.
• The default parameter values in SuperPang assume that all of the input genomes come from the same species (ANI>=0.95). This can be controlled by changing the values of the -i/--identity_threshold and -b/--bubble-identity-threshold to the expected ANI. However SuperPang has currently only been tested in species-level clusters.

Arguments

• -f/--fasta: Input fasta files with the sequences for each bin/genome, or a single file containing the path to one input fasta file per line.
• -q/--checkm: CheckM output for the bins. This can be the STDOUT of running checkm on all the fasta files passed in --fasta, or a tab-delimited file ended with a .tsv extension, in the form genome1 percent_completeness. Genome names should not contain the file extension (e.g. .fna). If empty, completeness will be estimated by mOTUpan but this may lead to wrong estimations for very incomplete genomes.
• -i/--identity_threshold: Identity threshold (fraction) to initiate correction with minimap2. Values of 1 or higher will skip the correction step entirely. Default 0.95.
• -m/--mismatch-size-threshold: Maximum contiguous mismatch size that will be corrected. Default 100.
• -g/--indel-size-threshold: Maximum contiguous indel size that will be corrected. Default 100.
• -r/--correction-repeats: Maximum iterations for sequence correction. Default 20.
• -n/--correction-repeats-min: Minimum iterations for sequence correction. Default 5.
• -k/--ksize: Kmer-size. Default 301.
• -l/--minlen: Scaffold length cutoff. Default 0 (no cutoff).
• -c/--mincov: Scaffold coverage cutoff. Default 0 (no cutoff).
• -b/--bubble-identity-threshold: Minimum identity (matches / length) required to remove a bubble in the sequence graph. Default 0.95.
• -a/--genome-assignment-threshold. Fraction of shared kmers required to assign a contig to an input genome (0 means a single shared kmer is enough). Default 0.5.
• -x/--default-completeness: Default genome completeness to assume if a CheckM output is not provided with --checkm. Default 70.
• -t/--threads: Number of processors to use. Default 1.
• -o/--output: Output directory. Default output.
• -d/--temp-dir: Directory for temp files. Default tmp.
• -u/--header-prefix: Prefix to be added to output sequence names. No prefix is added by default.
• --assume-complete: Assume that the input genomes are complete (--genome-assignment-threshold 0.95, --default-completeness 99).
• --lowmem: Use disk storages instead of memory when possible, reduces memory usage at the cost of execution time.
• --minimap2-path: Path to the minimap2 executable. Default minimap2.
• --keep-intermediate: Keep intermediate files.
• --keep-temporary: Keep temporary files.
• --verbose-mOTUpan: Print out mOTUpan logs.
• --nice-headers: Removes semicolons from non-branching-path names.
• --output-as-file-prefix: Use the output dir name also as a prefix for output file names.
• --force-overwrite: Write results even if the output directory already exists.
• --debug: Run additional sanity checks (increases execution time).

Output

• assembly.fasta: contigs.
• assembly.info: core/auxiliary and path information for each contig.
• NBPs.fasta: non-branching paths.
• NBPs.core.fasta: non-branching paths deemed to belong to the core genome of the species by mOTUpan.
• NBPs.accessory.fasta: non-branching paths deemed to belong to the accessory genome of the species.
• graph.fastg: assembly graph in a format compatible with bandage.
• NBP2origins.tsv: tab-separated file with the non-branching path IDs, a comma-separated list of the input sequences in which that NBP was deemed present, a comma-separated list of the input genomes in which that NBP was deemed present, and the number of input genomes in which that NBP was deemed present.
• params.tsv: parameters used in the run.

About

SuperPang is developed by Fernando Puente-Sánchez (Sveriges lantbruksuniversitet). Feel free to open an issue or reach out for support [e-mail].