Skip to content

Commit

Permalink
Merge pull request #5424 from AnnaSyme/patch-13
Browse files Browse the repository at this point in the history
Update tutorial.md - bacterial genomics QC
  • Loading branch information
bgruening authored Oct 9, 2024
2 parents 3395483 + 416e0d4 commit 3333297
Showing 1 changed file with 2 additions and 2 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -487,7 +487,7 @@ __Bracken__ (Bayesian Reestimation of Abundance after Classification with Kraken
> > <solution-title></solution-title>
> >
> > 1. 119, as the number of lines
> > 2. Staphylococcus, with 99.04%!
> > 2. Staphylococcaceae, with 99.06%!
> {: .solution}
>
{: .question}
Expand Down Expand Up @@ -610,4 +610,4 @@ Additionally, it's important to document and **report the contamination findings
In this tutorial, we inspected the quality of the bacterial isolate sequencing data and checked the expected species and potential contamination. Prepared short reads **can be used in downstream analysis**, like [Genome Assembly]({% link topics/assembly/tutorials/mrsa-illumina/tutorial.md %}). Even after the assembly, you can identify contamination using a tool like **CheckM** ({% cite Parks_2015 %}). **CheckM** {% icon tool %} can be used for screening the 'cleanness' of bacterial assemblies.
To learn more about data quality control, you can follow this tutorial: [Quality Control]({% link topics/sequence-analysis/tutorials/quality-control/tutorial.md %}).
To learn more about data quality control, you can follow this tutorial: [Quality Control]({% link topics/sequence-analysis/tutorials/quality-control/tutorial.md %}).

0 comments on commit 3333297

Please sign in to comment.