diff --git a/.shed.yml b/.shed.yml index def540f..4cad591 100644 --- a/.shed.yml +++ b/.shed.yml @@ -1,5 +1,5 @@ -name: autoBIGS -owner: RealYHD +name: autobigs +owner: ydeng description: Automated MLST typing from PubMLST and InstitutPasteur. homepage_url: https://github.com/Syph-and-VPD-Lab/autoBIGS.cli long_description: | diff --git a/README.md b/README.md new file mode 100644 index 0000000..55502b7 --- /dev/null +++ b/README.md @@ -0,0 +1,17 @@ + +# 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](https://pypi.org/project/autoBIGS.engine) via wrapping the official [autoBIGS.cli](https://github.com/Syph-and-VPD-Lab/autoBIGS.cli) wrapper. + +## Features + +This CLI is capable of exactly what [autoBIGS.engine](https://pypi.org/project/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