Comparative Genomics Analysis of Campylobacter jejuni

Genes were predicted by using the annotation pipeline Prokka (Seemann, 2014 (link)), which depend on Prodigal (Hyatt et al., 2010 (link)) for gene prediction. Core genome multi-locus sequence typing (cgMLST) was made using Ridom SeqSphere+, version 8.2.0, using the Oxford v.1 schema (Cody et al., 2017 (link)). Single-nucleotide polymorphism (SNP) analysis was made using Snippy,² version 4.0.2. The reference genome used for the SNP analysis was the GenBank C. jejuni reference NC002163.1. The percentage of the reference genome k-mers (20-mers) found in the assemblies was quantified using the tngs tool.

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Segerman B., Ástvaldsson Á., Mustafa L., Skarin J, & Skarin H. (2022). The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content. Frontiers in Microbiology, 13, 944770.

Publication 2022

SeqSphere

Gene Genome Mers Single nucleotide polymorphism

Corresponding Organization : Uppsala University

Other organizations : National Food Administration

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Variable analysis

independent variables

Gene prediction using Prokka and Prodigal
Core genome multi-locus sequence typing (cgMLST) using Ridom SeqSphere+
Single-nucleotide polymorphism (SNP) analysis using Snippy
Percentage of the reference genome k-mers (20-mers) found in the assemblies using the tngs tool

dependent variables

Predicted genes
Core genome sequence types
Single-nucleotide polymorphisms
Percentage of reference genome k-mers found in the assemblies

control variables

Reference genome used for SNP analysis (GenBank C. jejuni reference NC002163.1)

Annotations

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