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Fix British English
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contamination.qmd

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### recentrifuge
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Another popular tool for detecting contaminating microorganisms is [Recentrifuge](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006967). It works as a classifier that is trained to recognize contaminant microbial organisms. In case of Recentrifuge, one has to use blanks or other negative controls and provide microbial names and abundances on the blanks in order to train Recentrifuge to recognize endogenous vs. contaminant sources.
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Another popular tool for detecting contaminating microorganisms is [Recentrifuge](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006967). It works as a classifier that is trained to recognise contaminant microbial organisms. In case of Recentrifuge, one has to use blanks or other negative controls and provide microbial names and abundances on the blanks in order to train Recentrifuge to recognise endogenous vs. contaminant sources.
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### cuperdec
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## Questions to think about
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1. What is a false-positive microbial finding and how can we recognize it?
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1. What is a false-positive microbial finding and how can we recognise it?
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2. What is contamination and how can it bias ancient metagenomic analysis?
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3. What is a negative (blank) control sample and why is it useful to have?
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4. What is microbial source tracking and how can it help with decontamination?

genome-mapping.qmd

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## Examples
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Please find here a few examples for exploration. To get a better visualization we only loaded `sample2_lenient` (top track) and `sample2_strict` (bottom track):
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Please find here a few examples for exploration. To get a better visualisation we only loaded `sample2_lenient` (top track) and `sample2_strict` (bottom track):
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![](assets/images/chapters/genome-mapping/IGV_example_intro.png)
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