.. _glossary:

********
Glossary
********

.. glossary::

   Contig
      sequence...
   
   Scaffold
      sequence..
   
   Reads
      aaa
   
   BUSCO
      aaa
   
   ARIBA
      A
   
   NCBI Genbank
      adsasd
      
   BIGSdb
      asdads
   
   Pypi
      Python package index (Pypi, https://pypi.org/) is a repository of software for the 
      Python programming language.
   
   KMA
      adsad
   
   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).