annotate.Snakefile

A Snakemake pipeline to copy annotations between GenBank files

Usage

In-site pipeline

1. Clone the repository
2. Create a reference directory and put your reference sequences in it in Genbank format (i.e. reference/myseqs/seq1.gb, reference/myseqs/seq2.gb, ...)
3. Create an input directory and put your sequences in it in Genbank format.
4. Run snakemake.
5. Get your annotated sequences in the output directory.

With docker

docker run -v $(pwd):/input -v $(pwd):/output althonos/annotate

will annotate all the sequences in your current directory using the annotated sequences distributed with the moclo library.

Dependencies

• blast+ binaries (blastn and makeblastdb).
• snakemake
• biopython

About

This pipeline was developed by Martin Larralde for the data integration course of the AMI2B Master's degree of Université Paris-Sud.