Analysis performed on junio 06, 2023 at 11:41:22, using CamPype


Multi-Locus Sequence Typing (MLST)


Following table shows the Sequence Type (ST) and MLST allelic profile for each isolate using mlst.

Below each column name you will find a filter box that you can use to filter the table by columns. You can also filter by more than one column and export this new subset table into a separated file (see the export buttons available).


Back to index

Assembly analysis and annotation


Following table shows the number of contigs (> 200 bp), genome length, average contig length, N50, GC content (%) and depth coverage using SPAdes and annotation information using Prokka for each draft genome.

Below each column name you will find a filter box that you can use to filter the table by columns. You can also filter by more than one column and export this new subset table into a separated file (see the export buttons available).

Select the parameter

Number of contigs

Back to index

Draft genome length

Back to index

Average contig length

Back to index

N50

Back to index

GC Content

Back to index

Number of CDS

Back to index

Hypothetical proteins

Back to index

Number of CRISPRs

Back to index

Number of rRNAs

Back to index

Number of tRNAs

Back to index

Antibiotic resistance genes


Following table shows antibiotic resistance genes by screening the draft genomes against the Pathogen Detection Reference Gene Catalog by using AMRFinderPlus. Any hit with coverage below 80 % and identity below 60 % was removed.

Below each column name you will find a filter box that you can use to filter the table by columns. You can also filter by more than one column and export this new subset table into a separated file (see the export buttons available).


Following figure represents presence/absence of antibiotic resistance genes in each draft genome against the Pathogen Detection Reference Gene Catalog by using AMRFinderPlus. Presence is represented as minimum coverage of 80 % and minimum identity of 60 %.


Point mutations conferring antibiotic resistance

Resistance caused by point mutations is only included for Campylobacter spp. (and not for mixing genus)

Following table(s) show(s) antibiotic resistance genes by screening the draft genomes against the selected database(s) by using ABRicate. Any hit with coverage below 80 % and identity below 60 % was removed.

Below each column name you will find a filter box that you can use to filter the table by columns. You can also filter by more than one column and export this new subset table into a separated file (see the export buttons available).

Select the database

argannot
CARD
Megares
NCBI
Resfinder



Following figure(s) represent(s) presence/absence of antibiotic resistance genes in each draft genome against the selected database(s) by using ABRicate. Presence is represented as minimum coverage of 80 % and minimum identity of 60 %.

Select the database

argannot

card

megares

ncbi

resfinder



Back to index

Virulence Genes


Following table(s) show(s) virulence genes by screening the draft genomes against the selected database(s) by using ABRicate. Any hit with coverage below 80 % and identity below % was removed.

Below each column name you will find a filter box that you can use to filter the table by columns. You can also filter by more than one column and export this new subset table into a separated file (see the export buttons available).

Select the database

VFDB



Following figure represents presence/absence of virulence genes in each draft genome against the selected database(s) by using ABRicate. Presence is represented as minimum coverage of 80 % and minimum identity of 60 %.



Back to index

Plasmids


Following table(s) show(s) plasmids by screening the draft genomes against PlasmidFinder by using ABRicate. Any hit with coverage below 80 % and identity below 60 % was removed.

Below each column name you will find a filter box that you can use to filter the table by columns. You can also filter by more than one column and export this new subset table into a separated file (see the export buttons available).


Back to index

Pangenome analysis


Following charts show pangenome analysis with minimum 95 % identity for blastp using Roary.




Binary heatmap shows the presence (grey) and absence (white) of genes. Phylogeny for each isolate is shown on the left and was constructed based on accesory genes from the pangenome.

Back to index

Genomic variants


Following table shows genomic variants in each draft genome against the reference genome you indicated using Snippy.

Below each column name you will find a filter box that you can use to filter the table by columns. You can also filter by more than one column and export this new subset table into a separated file (see the export buttons available).


Back to index

Summary report


Following table shows summary information for each draft genome.

Below each column name you will find a filter box that you can use to filter the table by columns. You can also filter by more than one column and export this new subset table into a separated file (see the export buttons available).


Back to index

How to cite


Irene Ortega-Sanz, Jose A. Barbero and Antonio Canepa. CamPype (2023). Available at https://github.com/JoseBarbero/CamPype

Following packages and tools were used in CamPype:

Package/Tool Reference
QUAST v5.0.2 A. Gurevich et al., 2013
progressiveMauve v2.4.0 A.E. Darling et al., 2010
mlst v2.17.6 T. Seemann
ABRicate v1.0.1 T. Seemann
BLAST v2.9.0 Z. Zhang et al., 2000
AMRFinderPlus v3.11.2 M. Feldgarden et al., 2019
Prokka v1.14.6 T. Seemann, 2014
DFAST v1.2.4 Y. Tanizawa et al., 2018
Roary v3.12.0 A.J. Page et al., 2015
snippy v4.3.6 T. Seemann
ape v5.6-2 Paradis and Schliep, 2019
complexHeatmap v2.14.0 Gu et al., 2016
dplyr v1.0.10 Wickham et al., 2022
DT v0.26 Xie et al., 2022
ggplot2 v3.4.0 Wickham, 2016
ggtree v3.6.0 Yu et al., 2017
pander v0.6.5 Daróczi and Tsegelskyi, 2022
plotly v4.10.1 Sievert, 2020
rjson v0.2.21 Couture-Beil, 2022
rmarkdown v2.14 Allaire et al., 2022
tidyverse v1.3.2 Wickham et al., 2019

Back to index