Glossary¶
- Contig¶
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- Scaffold¶
sequence..
- Reads¶
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- BUSCO¶
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- ARIBA¶
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- NCBI Genbank¶
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- BIGSdb¶
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- Pypi¶
Python package index (Pypi, https://pypi.org/) is a repository of software for the Python programming language.
- KMA¶
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- reStructuredText (ReST)¶
reStructuredText format (http://docutils.sourceforge.net/rst.html). An easy-to-read, what-you-see-is-what-you-get plaintext markup syntax and parser system.
- Sphinx¶
Python module for documentation. See details in http://www.sphinx-doc.org/en/master/
- Edirect¶
Entrez direct (Edirect) provides access to the NCBI’s suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
Read further information of the Edirect utilities in https://www.ncbi.nlm.nih.gov/books/NBK179288/
- VFDB¶
The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is devoted to providing the scientific community with a comprehensive warehouse and online platform for deciphering bacterial pathogenesis.
- CARD¶
The Comprehensive Antibiotic Resistance Database (CARD, https://card.mcmaster.ca/) provides data, models, and algorithms relating to the molecular basis of antimicrobial resistance. The CARD provides curated reference sequences and SNPs organized via the Antibiotic Resistance Ontology (ARO).