Snakemake pipeline for gene prediction for Loxodes magnus, which has a genetic
code with context-dependent stop codons. Introns are first empirically
predicted with Intronarrator and
artifically removed to produce an "intronless" assembly, to run
Pogigwasc in --no-intron mode. This
is because the short lengths and unusual length distribution of introns in
Loxodes are difficult to model with the GHMM in Pogigwasc.
Pipeline and scripts to generate the genome assembly are available from loxodes-assembly-workflow repository. Pipeline for the "intronless" assembly is available from loxodes-intronarrator-workflow.
This current 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.