An annotation pipeline using snakemake that curently supports pfam, eggnog, tigrfam annotations.
To run:
-Create a directory for annotation
-Create a folder and put your original fasta files in
- module load python3.7-anaconda
-Run filtering script on a directory of bins
-This is required to filter out bins that do not meet the length requirement for running prodigal (20000 bases and prep the directory for the pipeline)
- Run: /nfs/turbo/lsa-dudelabs/pipelines/AnnotationPipeline/scripts/prep_annotation.py folder_of_fastas
- the script results in the creation of a directory called Passing_Bins in the directory the script is run from with all
bins linked in the directory that meet the length threshold.
- copy the config template from /nfs/turbo/lsa-dudelabs/pipelines/AnnotationPipeline/config_template.yaml and name it config.yaml.
- use the file extension in the Passing_Bins dir (fa or fna or fasta etc).
- module load singularity.
-Run Annotation.smk (I recommend putting this in a slurm script with 36 cores and 180gb mem for fastest run time).
singularity exec /nfs/turbo/lsa-dudelabs/pipelines/AnnotationPipeline/Singularity/annotation_tools.sif snakemake -s /nfs/turbo/lsa-dudelabs/pipelines/AnnotationPipeline/Annotation.smk --cores
Note on headers:
fasta headers cannot contain ":"