Genomic DNA from all strains of C. tetani was extracted and purified as previously described41 (link),42 . Whole genome sequencing (WGS) using the NEXTflex® PCR-Free DNA-Seq kit for Illumina Plaforms (Bioo Scientific Corporation) were performed using MiSeq device (Illumina) in paired-end reads of 250 or 300 bases. Sequence files were generated using Illumina Analysis Pipeline version 1.8 (CASAVA). Reads were trimmed using a quality control pipeline43 (link). The assembly of sequence reads was performed using SOAPdenovo (version 1.05).
Analysis pipeline version 1
Manufactured by Illumina
The Illumina Analysis Pipeline version 1.8 is a software tool that provides a comprehensive and integrated data analysis workflow for processing and analyzing sequencing data generated from Illumina platforms. The pipeline automates the various steps involved in the analysis of sequencing data, including read alignment, variant calling, and annotation.
Automatically generated - may contain errors
4 protocols using analysis pipeline version 1
1
Genome Sequencing of C. tetani
2
Whole Genome Sequencing with NEBNext Ultra
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Whole genome sequencing using the NEBNext Ultra DNA Library Prep kit for Illumina (New England Biolabs) were performed using MiSeq machine (Illumina) in paired-end reads of 250 bases or on HiSeq2000 machine (Illumina) in single reads of 96 bases or 101 bases. Sequence files were generated using Illumina Analysis Pipeline version 1.8 (CASAVA). After quality filtering, reads were assembled using CLC software version 4 (CLC Bio).
3
Whole Genome Sequencing of Yersinia pestis
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Whole genome sequencing of Y. pestis strains (Table 1 ) was performed using the NEXTflex PCR-Free DNA-Seq kit for Illumina (Bio Scientific), and a HiSeq2000 machine (Illumina, San Diego, CA) to yield paired-end reads of 100 bases. Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline version 1.8. Paired-end Fastq files were uploaded into the Yersinia database available in the Enterobase website (http://enterobase.warwick.ac.uk/ ). De novo assembly of the genomes and SNP calling against the CO92 reference genome (after correction according to Morelli et al., 2010) [30 ] were performed automatically using EnteroTools in the Enterobase website.
4
NextFlex PCR-free DNA Sequencing
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The libraries were generated using the NextFlex PCR-free DNA Seq Kit (Bioo Scientific, Austin, TX, USA) with (15 strains, with a two-letter and two-number code) or without (five strains, with a 20XX code) a 10-cycle PCR enrichment before quantification and validation. They were then sequenced on an Illumina MiSeq instrument in 250-base paired-end reads (Illumina, San Diego, CA, USA). Sequence files were generated using Illumina Analysis Pipeline version 1.8 (CASAVA).
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