MRG: cleanup on aisle 10 (#7)

* update AMR some more

* upd configuration script

* ssh key comment out

* hide @ctb

README.md

@@ -10,5 +10,6 @@ pip install -r requirements.txt
 
 and then either `mkdocs build` or `mkdocs serve`.
 
-Note, the website at @CTB will be automatically built.
-
+Note, the website at
+[ngs-docs.github.io/2024-pig-paradigm-workshop/](https://ngs-docs.github.io/2024-pig-paradigm-workshop/)
+will automatically build and deploy on merge to main.

configure.sh

@@ -2,19 +2,25 @@
 set -x
 set -e
 
+. /opt/miniconda3/etc/profile.d/conda.sh
+
+# add my ssh key
+echo ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBHFz3WLVqV+0md4OkZi/S0a79cOO7Ax8S4Dledp832JhMQ0GJ0ZlmEnWZrIv83KnRexpAEi5w6H1aSackGjucgQ= t@TitusMatsalmoth.attlocal.net >> ~/.ssh/authorized_keys
+
 mkdir ~/data/
 
 cd ~/data/
-curl -JLO http://farm.cse.ucdavis.edu/~ctbrown/transfer/IBD_tutorial_subset.tar.gz
-tar xzf IBD_tutorial_subset.tar.gz
-curl -JLO http://farm.cse.ucdavis.edu/~ctbrown/transfer/tutorial_other.tar.gz
-tar xzf tutorial_other.tar.gz
-
+#curl -JLO http://farm.cse.ucdavis.edu/~ctbrown/transfer/IBD_tutorial_subset.tar.gz
+tar xzf /opt/shared/IBD_tutorial_subset.tar.gz
+#curl -JLO http://farm.cse.ucdavis.edu/~ctbrown/transfer/tutorial_other.tar.gz
+tar xzf /opt/shared/tutorial_other.tar.gz
 
 mkdir ~/databases/
 cd ~/databases/
-curl -JLO https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-k31.zip
-curl -JLO https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214.lineages.csv.gz
+ln -fs /opt/shared/gtdb-rs214-k31.zip .
+ln -fs /opt/shared/gtdb-rs214.lineages.csv.gz .
+#curl -JLO https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-k31.zip
+#curl -JLO https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214.lineages.csv.gz
 
 cd ~/
 

docs/amr.md

@@ -1,20 +1,31 @@
 # Analyzing metagenomes for Antimicrobial Resistance (AMR) Genes
 
-## Install amrfinder, megahit, and prodigal.
+We're going to use
+[AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/),
+together with the
+[megahit metagenome assembler](https://github.com/voutcn/megahit) and
+the
+[prodigal gene finder](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-119),
+to look for antimicrobial resistance genes in the CD136 metagenome.
+
+We're going to do this by assembling the CD136 metagenome using the megahit
+assembler. This will give us contigs that represent the high coverage portion
+of the metagenome.
 
-@CTB links to software
+## Install amrfinder, megahit, and prodigal.
 
+First, install the software. Run:
 ```
 mamba create -n amrfinder -y ncbi-amrfinderplus megahit prodigal csvtk
 conda activate amrfinder
 ```
 
-Download the amrfinder database:
+Next, download the amrfinderplus database. Run:
 ```
 amrfinder -u
 ```
 
-and set up & change to a working directory:
+And, finally, set up & change to a working directory. Run:
 ```
 mkdir ~/amr/
 cd ~/amr/
@@ -24,7 +35,9 @@ cd ~/amr/
 
 We'll start by assembling the CD136 metagenome into contigs. In this
 case, we're not going to bin the contigs, because AMR genes
-[don't assemble well](https://www.biorxiv.org/content/10.1101/2023.12.13.571436v1.full).
+[don't assemble well](https://www.biorxiv.org/content/10.1101/2023.12.13.571436v1.full), and in particular don't assemble into regions that are
+connected to their host genome. So we run the assembler, and look at genes
+on the resulting contigs.
 
 Run:
 ```
@@ -44,14 +57,27 @@ This will produce a FASTA file containing many protein sequences:
 ```
 head CD136.assembly.faa
 ```
+These are the (partial & complete) genes found by the `prodigal` software.
 
 And, finally, run AMRfinder on the proteins:
 ```
-amrfinder -p CD136.assembly.faa -t 16 -o CD136.amrfinder.csv  --plus
+amrfinder -p CD136.assembly.faa -t 16 -o CD136.amrfinder.tsv --plus
+```
+
+This will produce a spreadsheet named `CD136.amrfinder.tsv` that
+contains a number of columns - you can see the list like so, using
+`csvtk headers`:
+
+```
+csvtk -t headers CD136.amrfinder.tsv
 ```
 
+To pick out just a few columns, you can use `csvtk cut`.
+
+Run:
 ```
-csvtk -t cut -f "% Coverage of reference sequence","HMM description" CD136.amrfinder.csv 
+csvtk -t cut -f "% Coverage of reference sequence","HMM description" CD136.amrfinder.tsv 
 ```
 
-@CTB examine output files.
+<!-- @CTB say something output the files.  -->
+

docs/comparing-metagenomes.md

@@ -17,11 +17,11 @@ cd ~/compare-metag
 
 ## Comparing based on content
 
-* reference free, annotation free @CTB
+<!-- * reference free, annotation free @CTB -->
 
 Here we are going to use the
 [`sourmash plot`](https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-plot-cluster-and-visualize-comparisons-of-many-signatures)
-command to compare and cluster many metagenomes based on their content.
+command to compare and cluster many metagenomes based on their content - not their annotation or assemblies.
 
 As with the [single metagenome analysis](single-metagenomes-taxonomy.md), we have two options here: with, or without abundance information.
 

docs/index.md

@@ -1,6 +1,6 @@
 # Introduction
 
-@CTB stuff about workshop
+<!-- @CTB stuff about workshop -->
 
 Tutorials: