Details of assembly methods and in silico genotyping for *Clostridioides* ========================================================================= * **All MLST-like typing methods in EnteroBase are derived from a genome assembly of sequenced reads. For an explanation of this method**, see :doc:`here ` * **For a general description of the in silico typing method**, see :doc:`here ` +-----------------+----------------+---------------+-----------------+ | MLST – Classic | Ribosomal MLST | Core Genome | Whole Genome | | | (Jolley, 2012) | MLST | MLST | +=================+================+===============+=================+ | 7 Loci | 53 Loci | 2,556 Loci | 11,490 Loci | +-----------------+----------------+---------------+-----------------+ | Conserved | Ribosomal | Core genes | Any coding | | Housekeeping | proteins | | sequence | | genes | | | | +-----------------+----------------+---------------+-----------------+ | Highly | Highly | Variable; | Highly | | conserved; Low | conserved; | High | variable; | | resolution | Medium | resolution | Extreme | | | resolution | | resolution | +-----------------+----------------+---------------+-----------------+ | Different | Single scheme | Different | Different | | scheme for each | across tree of | scheme for | scheme for each | | species/genus | life | each | species/genus | | | | species/genus | | +-----------------+----------------+---------------+-----------------+ 7 Gene MLST ----------- The classic MLST scheme for Clostridioides is described in `Griffiths et al (2010) J. Clin. Microbiol. 48, 770-778`_. Genes included in 7 gene MLST (together with the length of sequence used for MLST taken from table 1 in the above cited paper): ==== ====== Gene Length ==== ====== adk 501 atpA 555 dxr 411 glyA 516 recA 564 sodA 450 tpi 504 ==== ====== Ribosomal MLST (rMLST) ---------------------- - **rMLST** is Copyright © 2010-2016, University of Oxford. rMLST is described in `Jolley et al. 2012 Microbiology 158:1005-15`_. .. _please click here: EnteroBase%20Backend%20Pipeline%3A%20nomenclature .. _Griffiths et al (2010) J. Clin. Microbiol. 48, 770-778: http://dx.doi.org/10.1128%2FJCM.01796-09 .. _`Jolley et al. 2012 Microbiology 158:1005-15`: http://www.ncbi.nlm.nih.gov/pubmed/22282518