autoBIGS.Galaxy

A program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST. autoBIGS.galaxy is the galaxy frontend implementation of autoBIGS.cli and autoBIGS.engine.

This Galaxy tool implements autoBIGS.engine via wrapping the official autoBIGS.cli wrapper.

Features

This CLI is capable of exactly what autoBIGS.engine is capable of:

• Import multiple whole genome FASTA files
• Fetch the available BIGSdb databases that is currently live and available
• Fetch the available BIGSdb database schemas for a given MLST database
• Retrieve exact/non-exact MLST allele variant IDs based off a sequence
• Retrieve MLST sequence type IDs based off a sequence
• Inexact matches are annotated with an asterisk (*)
• Output all results to a single CSV