A command-line interface based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV.
2. Once installation is complete, run `autoBIGSst --version` to test that the installation succeeded (and that you are running the appropriate version).
Let's say you have a fasta called `seq.fasta` which contains several sequences. You know all sequences in `seq.fasta` are Bordetella pertussis sequences, and you know you have the sequences for the necessary targets of your schema in each of them. You want to retrieve MLST profiles for all of them. This can be done by:
1. Running `autoBIGSst info -l` to list all available `seqdef` databases and find the database associated with Bordetella (you should see one called `pubmlst_bordetella_seqdef`).
2. Then, run `autoBIGSst info -lschema pubmlst_bordetella_seqdef` to get the available typing schemas and their associated IDs. In this example, let's assume we want a normal MLST scheme. In this case, we would pay attention to the number next to `MLST` (it should be `3`).
4. Namely, you should find that you will need to run `autoBIGSst st seq.fasta pubmlst_bordetella_seqdef 3 output.csv`. You can optionally include multiple `FASTA` files, and/or `--exact` to only retrieve exact sequence types, and/or `--stop-on-fail` to stop typing if one of your sequences fail to retrieve any type.
