Hanel 2018
Summary table
| Key | Value |
|---|---|
| category | read-based |
| platform | illumina |
| open source | true |
| reproducible | false |
| documented | false |
Database
This protocol uses ResFinderfor detection of AMR genes in A. skirrowii. Database version not mentioned.
Protocol
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Step 1 DNA was purified using High Pure PCR Template Preparation Kit and sequencing libraries were generated using the Nextera XT DNA Library Prep Kit.
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Step 2 Paired-end reads were generated using Illumina MiSeq
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Step 3 Further read processing included quality trimming and assembly with SPAdes 3.9.1 and filtering by removing contigs with a coverage < 5 and a length < 500. Quality was assessed with QUAST 4.3
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Step 4 Annotation was performed with Prokka using the recommended standard settings.
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Step 5 Resistance genes were predicted using the ResFinder
Citation
The paper(s) documenting this protocol:
- Hanel I et al. Antimicrobial Susceptibility and Genomic Structure of Arcobacter skirrowii Isolates. Front Microbiol. 2018
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