FOAM

FOAM (Flye ONT Assembly of Mitogenomes). Is a pipeline we have been using to assemble the complete circular mitogenome of different organisms. Although previous versions used a combination of Illumina and ONT reads, due to the increased accuracy of the latest we are only using ONT Q20+ reads. Keep in mind that as each genome and sample poses different challenges is in continuous development.

Current release

Version 0.7 is now available. You can look for previous releases using the corresponding tag.

Taxonomic range

FOAM has been used to assemble the mitogenomes of several ERGA-BGE species. It has been successful across different taxa including insects, sponges, archnids and vertebrates. Previous versions were used in various genomes, see some the publications below.

Workflow

FOAM Snakemake rulegraph summarizing all the steps.

To make it run

1. Clone this repository.
2. Download the refseq81 databases from https://zenodo.org/records/2672835
3. Copy them to your local utils/refseq_dir.
4. Uncompress the refseq databases locally (example: tar jvxf refseq81m.tar.bz2). This will allow you to run mitos stand-alone without using the web interface.
5. Create config files for your genome. For that (check examples/config forlder config.yamls and also the foam.cnag_cluster.yaml that works for our slurm cluster in example/configs).
6. Run the pipeline with snakemake pointing to the snakefile in bin.

Config and key parameters

• Reference Length: Set the right length for the reference genome used, example reference_length: 15025 for NC_012901 (i.e. Blattella germanica used as reference for Loboptera ibLobCana)

• Genetic Code: Chose the appropriate genetic code: 2 for Vertebrate 5 for Invertebrate (check code in Genetic_Code_Mitos.txt placed in the utils/ folder)

• Mapping and Assembly As v0.5 expects ONT Q20+ reads or hifi reads, it will no longer use Illumina data for polishing. Therefore mapping and assembly options below are adapted to long reads of high accuracy. These values should work for most species:

  parameters: max_read_length: 18000 ontfilter_minmatch: 5000 ontfilter_minq: 15 minimap2_opts: " -ax map-hifi" flye_opts: " --meta --scaffold -i 1" flye_reads: " --nano-hq" polishing_flye: "-i 1" mito_length_variation: 2000 tolid: ibLobCana

  Key parameters to tweak are ontfilter_minmatch and ontfilter_minq: depending on the coverage and divergence to the reference, they could be increased to ensure detection of reads with larger and/or more unique alignments to the reference. Therefore, this can ensure the correct circularization of the contig. For example, we had to run it on mMarFoi with a higher value (i.e. 12,000) to obtain a circular contig of the expected size +- 2,000 bp.

Contributors

Fernando Cruz, Jèssica Gómez-Garrido and Tyler Alioto. Genome Assembly and Annotation Team (CNAG).

Visit our website for more info about the team: https://denovo.cnag.cat/about

References

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797) Dalila Destanović, ProfileDarrin T. Schultz, Ruth Styfhals, Fernando Cruz, Jèssica Gómez-Garrido, Marta Gut, Ivo Gut, Graziano Fiorito, Oleg Simakov, Tyler S. Alioto, Giovanna Ponte, Eve Seuntjens. doi: https://doi.org/10.1101/2023.05.16.540928