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

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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).