Harrison Deng
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Markdown
18 lines
1.0 KiB
Markdown
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# autoBIGS.Galaxy
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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.
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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.
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## Features
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This CLI is capable of exactly what [autoBIGS.engine](https://pypi.org/project/autoBIGS.engine) is capable of:
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- Import multiple whole genome FASTA files
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- Fetch the available BIGSdb databases that is currently live and available
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- Fetch the available BIGSdb database schemas for a given MLST database
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- Retrieve exact/non-exact MLST allele variant IDs based off a sequence
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- Retrieve MLST sequence type IDs based off a sequence
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- Inexact matches are annotated with an asterisk (\*)
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- Output all results to a single CSV
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