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| Dear course participants,
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| In this exercise you will analyse microbial genome sequences using bioinformatics tools that are commonly used for microbial diagnostics and research.
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| == Background ==
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| We imagine that we are employed at a hospital to provide diagnostics for patient care.
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| The laboratory has sequenced genomic DNA from a clinical specimen. The sequence reads are stored in FASTQ files that are compressed with gzip:
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| * X
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| * Y
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| Use the following command to read the first lines of one of the files and inspect its content:
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| <pre>
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| zcat filename.fastq.gz | head
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| </pre>
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| == EX02: What species is it? ==
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| The laboratory has sequenced genomic DNA from single-colony isolates of bacteria cultivated from a clinical specimen. The sequence reads have been ''de novo'' assembled, and the genome assemblies are stored in FASTA-formatted files:
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| * X
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| === Task ===
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| Your goal is to determine the bacterial species of the assembled genomes.
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| You can use the '''Genome Taxonomy Database (GTDB)''' to determine the species assignment.
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| === Reference ===
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| [https://teaching.healthtech.dtu.dk/22126/images/c/cd/Gtdbtk.pdf GTDB-Tk tutorial (PDF)]
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