Fragmented Giardia DNA (2 μg, 550 bp insert size) from the trophozoites was first prepared and indexed using Illumina TruSeq DNA PCR-Free Sample Prep Kit (Cat. Nr 20015962 and 20015960S). Library size distribution was validated using the Agilent Technologies 2100 BioAnalyzer, High Sensitivity DNA chip, and quantification was done using the KAPA Library Quantification Kit for Illumina sequencing platforms. Normalized whole genome Giardia DNA-libraries were sequenced using the Illumina MiSeq paired-end technology (2×300 bp). FASTQ-files from the sequencing were assembled and aligned to the corresponding reference genomes of Giardia assemblage A2 and B (v.26) using Bowtie 2-2.2.3.51 (link) The reference genomes were obtained from Giardia DB in January 2016 versions 2013-11-25.52 (link)
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Whole-Genome Sequencing of Giardia
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Corresponding Organization : Haukeland University Hospital
Other organizations : Robert Koch Institute, University of Oulu, Haraldsplass Diakonale Sykehus
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Variable analysis
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- Fragmented Giardia DNA (2 μg, 550 bp insert size) from the trophozoites
- Normalized whole genome Giardia DNA-libraries sequenced using the Illumina MiSeq paired-end technology (2×300 bp)
- FASTQ-files from the sequencing assembled and aligned to the corresponding reference genomes of Giardia assemblage A2 and B (v.26)
- Illumina TruSeq DNA PCR-Free Sample Prep Kit (Cat. Nr 20015962 and 20015960S) used for library preparation and indexing
- Library size distribution validated using the Agilent Technologies 2100 BioAnalyzer, High Sensitivity DNA chip
- Quantification done using the KAPA Library Quantification Kit for Illumina sequencing platforms
- Reference genomes of Giardia assemblage A2 and B (v.26) obtained from Giardia DB in January 2016 versions 2013-11-25
- Bowtie 2-2.2.3.51 used for sequence alignment
- No positive or negative controls were explicitly mentioned in the provided information.
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