FOAM (Flye ONT Assembly of Mitogenomes). Is a pipeline we are using to assemble the mitogenome of different organisms using ONT and Illumina reads. As each genome and sample poses different challenges is in continuous development. Thisrepository was originally posted and will be actively updated in our assembly team's github: https://github.com/cnag-aat/FOAM
Version 0.2 was successfully used to assemble the mitogenomes of the pearl razorfish (Xyrichtys novacula) and the common octopus (Octopus vulgaris).
To make it run:
- Clone this repository.
- Go to your local utils/refseq_dir.
- 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.
- Create config files for your genome (check the X. novacula example .yaml and .spec for a slurm cluster in example/configs).
- Run the pipeline with snakemake pointing to the snakefile in bin.
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
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