BejaLab's fosmid assembly and annotation pipeline

The pipeline takes the list of fosmids in fosmids.txt that contains three columns: fosmid name and left and right reads.

The pipeline will run:

• quality trimming with trim_galore
• assembly with spades
• vector trimming with cutadapt (the vector flanks are specified in workflow/metadata/vector_{fw,rv}.fna)
• annotation with pgap (using default metadata for Escherichia coli)
• conversion to .tbl with gbf2tbl.pl (from NCBI)

The main output files are:

• analysis/fosmids/{id}.fna -- trimmed fosmid sequence
• analysis/fosmids/{id}.info -- vector trimming report
• analysis/pgap/{id}/annot.tbl -- annotations in .tbl format
• analysis/pgap/{id}/annot.gbf -- annotations in .tbl format

How to run:

• add fosmids to fosmids.txt
• check that the raw data are there
• run: snakemake -c{threads} --use-conda