Merge pull request #99 from SPAAM-community/genome-mapping-corrections

Genome mapping corrections post-review corrections

Author: jfy133

assets/references/genome-mapping.bib

@@ -71,4 +71,50 @@ @article{Cingolani2012
   year = {2012},
   month = apr,
   pages = {80–92}
-}
+}
+
+@ARTICLE{Bos2014-xe,
+  title    = "Pre-Columbian mycobacterial genomes reveal seals as a source of
+              New World human tuberculosis",
+  author   = "Bos, Kirsten I and Harkins, Kelly M and Herbig, Alexander and
+              Coscolla, Mireia and Weber, Nico and Comas, Iñaki and Forrest,
+              Stephen A and Bryant, Josephine M and Harris, Simon R and
+              Schuenemann, Verena J and Campbell, Tessa J and Majander, Kerttu
+              and Wilbur, Alicia K and Guichon, Ricardo A and Wolfe Steadman,
+              Dawnie L and Cook, Della Collins and Niemann, Stefan and Behr,
+              Marcel A and Zumarraga, Martin and Bastida, Ricardo and Huson,
+              Daniel and Nieselt, Kay and Young, Douglas and Parkhill, Julian
+              and Buikstra, Jane E and Gagneux, Sebastien and Stone, Anne C and
+              Krause, Johannes",
+  journal  = "Nature",
+  volume   =  514,
+  number   =  7523,
+  pages    = "494--497",
+  abstract = "Modern strains of Mycobacterium tuberculosis from the Americas are
+              closely related to those from Europe, supporting the assumption
+              that human tuberculosis was introduced post-contact. This notion,
+              however, is incompatible with archaeological evidence of
+              pre-contact tuberculosis in the New World. Comparative genomics of
+              modern isolates suggests that M. tuberculosis attained its
+              worldwide distribution following human dispersals out of Africa
+              during the Pleistocene epoch, although this has yet to be
+              confirmed with ancient calibration points. Here we present three
+              1,000-year-old mycobacterial genomes from Peruvian human
+              skeletons, revealing that a member of the M. tuberculosis complex
+              caused human disease before contact. The ancient strains are
+              distinct from known human-adapted forms and are most closely
+              related to those adapted to seals and sea lions. Two independent
+              dating approaches suggest a most recent common ancestor for the M.
+              tuberculosis complex less than 6,000 years ago, which supports a
+              Holocene dispersal of the disease. Our results implicate sea
+              mammals as having played a role in transmitting the disease to
+              humans across the ocean.",
+  month    =  oct,
+  year     =  2014,
+  url      = "http://dx.doi.org/10.1038/nature13591",
+  doi      = "10.1038/nature13591",
+  pmc      = "PMC4550673",
+  pmid     =  25141181,
+  issn     = "0028-0836,1476-4687",
+  language = "en"
+}

authentication.qmd

@@ -1011,6 +1011,38 @@ And click "Open folder"
 You can double-click on the pdf files to visualise them.
 :::
 
+
+## (Optional) clean-up
+
+Let's clean up our working directory by removing all the data and output from this chapter.
+
+The command below will remove the `/<PATH>/<TO>/authentication` _as well as all of its contents_. 
+
+::: {.callout-tip}
+## Pro Tip
+Always be VERY careful when using `rm -r`.
+Check 3x that the path you are specifying is exactly what you want to delete and nothing more before pressing ENTER!
+:::
+
+```bash
+rm -r /<PATH>/<TO>/authentication*
+```
+
+Once deleted we can move elsewhere (e.g. `cd ~`).
+
+We can also get out of the `conda` environment with.
+
+```bash
+conda deactivate
+```
+
+Then to delete the conda environment.
+
+```bash
+conda remove --name authentication --all -y
+```
+
+
 ## Summary
 
 In addition, we:

contamination.qmd

@@ -121,7 +121,7 @@ Let us now discuss a few available computational approaches to decontaminate met
 
 ### recentrifuge
 
-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.
+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.
 
 ### cuperdec
 
@@ -436,7 +436,7 @@ In this chapter we have learned that:
 
 ## Questions to think about
 
-1. What is a false-positive microbial finding and how can we recognize it?
+1. What is a false-positive microbial finding and how can we recognise it?
 2. What is contamination and how can it bias ancient metagenomic analysis?
 3. What is a negative (blank) control sample and why is it useful to have?
 4. What is microbial source tracking and how can it help with decontamination?