Snakemake pipeline to empirically annotate introns and produce an artificial "intronless" genome sequence with Intronarrator for downstream gene prediction.
Genome assembly is available from the European Nucleotide Archive under accession PRJEB55123; RNA-seq data under accession PRJEB55324.
Pipeline and scripts to generate the genome assembly and RNA-seq mapping are available from loxodes-assembly-workflow repository.
The same pipeline was used for annotation of the MAC and MIC genomes; path to reference assembly and names of output files were modified accordingly.
Paths to input files in the workflow/config.yaml file are local paths used in
the original data analysis. When re-running the pipeline, replace these with
the actual paths on your system.
Curated output from this annotation are included in the archive of genome annotations.
To run on a local server, use ./run_snakemake.sh script, and add rule names
and additional parameters, e.g. ./run_snakemake.sh --dryrun.