Minor fixes to acecesing-metagenomic-data

Author: jfy133

accessing-ancient-metagenomic-data.qmd

@@ -355,26 +355,30 @@ First we can download the ancientsinglegenome-hostassociated samples table with
 AMDirT download -t ancientsinglegenome-hostassociated -y samples
 ```
 
-This will produce a file called `ancientsinglegenome-hostassociated_samples_v24.03.0.tsv` in your current directory (by default).
+This will produce a file called `ancientsinglegenome-hostassociated_samples_<DATA_VERSION>.tsv` in your current directory (by default).
+
+::: {.callout-warning}
+You will need to replace `<DATA_VERSION>` with the version number of the AncientMetagenomeDir release you are using in all commands of this tutorial!
+:::
 
 ```bash
 ls
 ```
 ```{verbatim}
-ancientsinglegenome-hostassociated_samples_v24.03.0.tsv
+ancientsinglegenome-hostassociated_samples_<DATA_VERSION>.tsv
 ```
 
 Then we can use a bit of bash to filter the table in the same way as we did in the GUI.
 In this command, we tell `awk` that the column separator is a tab, print the row if either it's the first record (line of the file), or if column one matches `Muhlemann2020` and column seven matches `Norway`.
 
 ```bash
-awk -F "\t" 'NR==1 || $1 == "Muhlemann2020" && $7 == "Norway"' ancientsinglegenome-hostassociated_samples_v24.03.0.tsv > ancientsinglegenome-hostassociated_samples_v24.03.0_filtered.tsv
+awk -F "\t" 'NR==1 || $1 == "Muhlemann2020" && $7 == "Norway"' ancientsinglegenome-hostassociated_samples_<DATA_VERSION>.tsv > ancientsinglegenome-hostassociated_samples_<DATA_VERSION>_filtered.tsv
 ```
 
 Then, we can pass this filtered table to the `AMDirT convert` command to firstly retrieve the library-level metadata.
 
 ```bash
-AMDirT convert --librarymetadata ancientsinglegenome-hostassociated_samples_v24.03.0_filtered.tsv ancientsinglegenome-hostassociated
+AMDirT convert --librarymetadata ancientsinglegenome-hostassociated_samples_<DATA_VERSION>_filtered.tsv ancientsinglegenome-hostassociated
 ```
 
 This has downloaded a new file called `AncientMetagenomeDir_filtered_libraries.tsv`, which we can then further filter in the same away to match the desired libraries as we picked during the GUI section of the tutorial!
@@ -386,7 +390,7 @@ awk -F "\t" 'NR==1 || $14 == "Targeted-Capture"' AncientMetagenomeDir_filtered_l
 Then with these two filtered files, one for samples,and one for libraries, we can supply them to the `convert` command to generate the same download scripts, eager input samplesheet, and citation `.bib` file as we did before!
 
 ```bash
-AMDirT convert -o . --bibliography --curl --eager --libraries AncientMetagenomeDir_filtered_libraries_capturedonly.tsv ancientsinglegenome-hostassociated_samples_v24.03.0_filtered.tsv ancientsinglegenome-hostassociated
+AMDirT convert -o . --bibliography --curl --eager --libraries AncientMetagenomeDir_filtered_libraries_capturedonly.tsv ancientsinglegenome-hostassociated_samples_<DATA_VERSION>_filtered.tsv ancientsinglegenome-hostassociated
 ```
 
 You should see a few messages saying `Writing <XYZ>`, and then if we run `ls`, you should see the same resulting files starting with `AncientMetagenomeDir_` as before with the GUI!
@@ -401,32 +405,32 @@ AncientMetagenomeDir_curl_download_script.sh
 AncientMetagenomeDir_filtered_libraries.tsv
 AncientMetagenomeDir_filtered_libraries_capturedonly.tsv
 AncientMetagenomeDir_nf_core_eager_input_table.tsv
-ancientsinglegenome-hostassociated_samples_v24.03.0.tsv
-ancientsinglegenome-hostassociated_samples_v24.03.0_filtered.tsv
+ancientsinglegenome-hostassociated_samples_<DATA_VERSION>.tsv
+ancientsinglegenome-hostassociated_samples_<DATA_VERSION>_filtered.tsv
 ```
 
 Therefore the `convert` command route of AMDirT allows you to include AMDirT in more programmatic workflows to make downloading data more efficiently.
 
 ### AMDirT Practise
 
 ::: {.callout-tip title="Question" appearance="simple"}
-Try to use your preferred AMDirT interface (GUI or CLI) to find the number of all single-stranded libraries of dental calculus _metagenomes_, published since 2021
+Try to use your preferred AMDirT interface (GUI or CLI) to find the number of all single-stranded libraries of palaeofaeces _metagenomes_, published since 2021
 :::
 
 ::: {.callout-note collapse="true" title="Answer"}
-The answer is 16 libraries across 2 publications: Klapper et al. [-@Klapper2023-nv] and Fotani et al. [-@Fontani2023-io]
+The answer is 19 libraries across 1 publications: Maixner 2021 [-@Maixner2021-sg]
 
 You can calculate this with the CLI method as follows.
 
 ```bash
 ## Download the ancient metagenome table
 AMDirT download -t ancientmetagenome-hostassociated -y samples
 
-## Filter to just dental calculus since 2021
-awk -F "\t" 'NR==1 || $2 >= 2021 && $13 == "dental calculus"' ancientmetagenome-hostassociated_samples_v24.03.0.tsv > ancientmetagenome-hostassociated_samples_v24.03.0_filtered.tsv
+## Filter to just palaeofaeces since 2021
+awk -F "\t" 'NR==1 || $2 >= 2021 && $13 == "palaeofaeces"' ancientmetagenome-hostassociated_samples_<DATA_VERSION>.tsv > ancientmetagenome-hostassociated_samples_<DATA_VERSION>_filtered.tsv
 
 ## Get the library metadata of the dental calculus (might take a little bit of time)
-AMDirT convert --librarymetadata ancientmetagenome-hostassociated_samples_v24.03.0_filtered.tsv ancientmetagenome-hostassociated
+AMDirT convert --librarymetadata ancientmetagenome-hostassociated_samples_<DATA_VERSION>_filtered.tsv ancientmetagenome-hostassociated
 
 ## Filter to just single stranded libraries
 awk -F "\t" 'NR==1 || $9 == "single"' AncientMetagenomeDir_filtered_libraries.tsv > AncientMetagenomeDir_filtered_libraries_singlestranded.tsv
@@ -491,7 +495,6 @@ We are forking a personal fork of the main repository to ensure we don't acciden
 3. **Switch** to a new branch called `dev`
 
 	```bash
-
 	git switch -c dev
 	```
 

assets/references/accessing-ancient-metagenomic-data.bib

@@ -493,3 +493,49 @@ @article{Klapper2023-nv
   issn      = {0036-8075,1095-9203},
   language  = {en}
 }
+
+@article{Maixner2021-sg,
+  title    = {Hallstatt miners consumed blue cheese and beer during the Iron Age
+              and retained a non-Westernized gut microbiome until the Baroque
+              period},
+  author   = {Maixner, Frank and Sarhan, Mohamed S and Huang, Kun D and Tett,
+              Adrian and Schoenafinger, Alexander and Zingale, Stefania and
+              Blanco-Míguez, Aitor and Manghi, Paolo and Cemper-Kiesslich, Jan
+              and Rosendahl, Wilfried and Kusebauch, Ulrike and Morrone, Seamus
+              R and Hoopmann, Michael R and Rota-Stabelli, Omar and Rattei,
+              Thomas and Moritz, Robert L and Oeggl, Klaus and Segata, Nicola
+              and Zink, Albert and Reschreiter, Hans and Kowarik, Kerstin},
+  journal  = {Current biology: CB},
+  abstract = {We subjected human paleofeces dating from the Bronze Age to the
+              Baroque period (18th century AD) to in-depth microscopic,
+              metagenomic, and proteomic analyses. The paleofeces were preserved
+              in the underground salt mines of the UNESCO World Heritage site of
+              Hallstatt in Austria. This allowed us to reconstruct the diet of
+              the former population and gain insights into their ancient gut
+              microbiome composition. Our dietary survey identified bran and
+              glumes of different cereals as some of the most prevalent plant
+              fragments. This highly fibrous, carbohydrate-rich diet was
+              supplemented with proteins from broad beans and occasionally with
+              fruits, nuts, or animal food products. Due to these traditional
+              dietary habits, all ancient miners up to the Baroque period have
+              gut microbiome structures akin to modern non-Westernized
+              individuals whose diets are also mainly composed of unprocessed
+              foods and fresh fruits and vegetables. This may indicate a shift
+              in the gut community composition of modern Westernized populations
+              due to quite recent dietary and lifestyle changes. When we
+              extended our microbial survey to fungi present in the paleofeces,
+              in one of the Iron Age samples, we observed a high abundance of
+              Penicillium roqueforti and Saccharomyces cerevisiae DNA.
+              Genome-wide analysis indicates that both fungi were involved in
+              food fermentation and provides the first molecular evidence for
+              blue cheese and beer consumption in Iron Age Europe.},
+  month    = oct,
+  year     = 2021,
+  url      = {http://dx.doi.org/10.1016/j.cub.2021.09.031},
+  keywords = {Hallstatt; beer; cheese; diet; fermented food; microbiome;
+              paleofeces; protohistory; salt mine},
+  doi      = {10.1016/j.cub.2021.09.031},
+  pmid     = 34648730,
+  issn     = {0960-9822,1879-0445},
+  language = {en}
+}