Tools

This page is intended for me to keep records of scripts that I’ve written.

To be updated.

Convert gbk (GenBank files) to csv:

• Tutorial: gbk to csv
• Python script: extract_gbk_to_csv.py

Convert breseq output to csv using gdtools:

• Tutorial: breseq parser gdtools
• Python script: breseq_parser_gdtools.py
• Example shell script to run python script on beagle: breseq_parser_gdtools.sh

Compare amino acid sequence of homologous loci (i.e. multiple sequence align; MSA) across several Genbank files and output summary of differences as a csv:

• Under construction

Work in Progress:

Convert Genbank (gbk) files to Roary-acceptable gff3 file:

• Coming soon. You can use this tool to convert a gbk file to Roary-acceptable gff3 file without having to run Prokka.