Genome Overview

This page provide multiple data about your organism:

• Starting with general data (Gram, Taxonomy, genome length …).

• Then, the GTDB-tk taxonomic classification is shown, along with the method used [1].

• CheckM and CheckM2 analysis results are presented, to assess the quality of microbial genomes in terms of completeness and contamination [2] [3].

• And some general statistical data about a replicon, such as: Length, GC%, Ribosomal RNAs, tRNAs types, Annotations Status, Average CDS length, Repeated regions, Average intergenic length , Protein coding density, Scaffolds/Contigs numbers, etc.

[1]

Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks, GTDB-Tk v2: memory friendly classification with the genome taxonomy database, Bioinformatics, Volume 38, Issue 23, 1 December 2022, Pages 5315–5316,

[2]

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. *CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes*. Genome Research, 25: 1043–1055.

[3]

Chklovski, A., Parks, D.H., Woodcroft, B.J. et al. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods 20, 1203–1212 (2023).