Assembly pipeline from 10x chromium reads from the preprint "Three new genome assemblies of blue mussel lineages: North and South European Mytilus edulis and Mediterranean Mytilus galloprovincialis" bioRxiv (https://doi.org/10.1101/2022.09.02.506387).

snakemake (in a conda environnement for example) and singularity need to be installed.

Supernova use large amount of storage for temporary and final results.

The supernova results are stored on a distant NAS that needs to be mounted first on my system.

sshfs nas4:/share/sea/sea/projects/ref_genomes/assembly_10x/results/supernova_assemblies \
results/supernova_assemblies \
-o idmap=user,compression=no,uid=1000,gid=1000,allow_root

I also used a 4T disk as a temporary local storage for supernova computation sudo mount /dev/sd[x]1 /data/ref_genomes/assembly_10x/tmp

To run use:

conda activate snake_env

snakemake --use-conda \
--use-singularity --singularity-args "-B /nas_sea:/nas_sea" \
-j {threads} \
[either all_v6, asm_improvement, stats, repeats, annotation, finalize or ncbi_submission (see workflow/Snakefile)]