From 5278be349a76f05f72fdf9f78c85eac957bd7a35 Mon Sep 17 00:00:00 2001 From: <> Date: Mon, 29 Apr 2024 12:46:20 +0000 Subject: [PATCH] Deployed 1eddf40 with MkDocs version: 1.6.0 --- .nojekyll | 0 404.html | 511 ++ amr/index.html | 753 ++ assets/images/favicon.png | Bin 0 -> 1870 bytes assets/javascripts/bundle.dd8806f2.min.js | 29 + assets/javascripts/bundle.dd8806f2.min.js.map | 7 + assets/javascripts/lunr/min/lunr.ar.min.js | 1 + assets/javascripts/lunr/min/lunr.da.min.js | 18 + assets/javascripts/lunr/min/lunr.de.min.js | 18 + assets/javascripts/lunr/min/lunr.du.min.js | 18 + assets/javascripts/lunr/min/lunr.el.min.js | 1 + assets/javascripts/lunr/min/lunr.es.min.js | 18 + assets/javascripts/lunr/min/lunr.fi.min.js | 18 + assets/javascripts/lunr/min/lunr.fr.min.js | 18 + assets/javascripts/lunr/min/lunr.he.min.js | 1 + assets/javascripts/lunr/min/lunr.hi.min.js | 1 + assets/javascripts/lunr/min/lunr.hu.min.js | 18 + assets/javascripts/lunr/min/lunr.hy.min.js | 1 + assets/javascripts/lunr/min/lunr.it.min.js | 18 + assets/javascripts/lunr/min/lunr.ja.min.js | 1 + assets/javascripts/lunr/min/lunr.jp.min.js | 1 + assets/javascripts/lunr/min/lunr.kn.min.js | 1 + assets/javascripts/lunr/min/lunr.ko.min.js | 1 + assets/javascripts/lunr/min/lunr.multi.min.js | 1 + assets/javascripts/lunr/min/lunr.nl.min.js | 18 + assets/javascripts/lunr/min/lunr.no.min.js | 18 + assets/javascripts/lunr/min/lunr.pt.min.js | 18 + assets/javascripts/lunr/min/lunr.ro.min.js | 18 + assets/javascripts/lunr/min/lunr.ru.min.js | 18 + assets/javascripts/lunr/min/lunr.sa.min.js | 1 + .../lunr/min/lunr.stemmer.support.min.js | 1 + assets/javascripts/lunr/min/lunr.sv.min.js | 18 + assets/javascripts/lunr/min/lunr.ta.min.js | 1 + assets/javascripts/lunr/min/lunr.te.min.js | 1 + assets/javascripts/lunr/min/lunr.th.min.js | 1 + assets/javascripts/lunr/min/lunr.tr.min.js | 18 + assets/javascripts/lunr/min/lunr.vi.min.js | 1 + assets/javascripts/lunr/min/lunr.zh.min.js | 1 + assets/javascripts/lunr/tinyseg.js | 206 + assets/javascripts/lunr/wordcut.js | 6708 +++++++++++++++++ .../workers/search.b8dbb3d2.min.js | 42 + .../workers/search.b8dbb3d2.min.js.map | 7 + assets/stylesheets/main.66ac8b77.min.css | 1 + assets/stylesheets/main.66ac8b77.min.css.map | 1 + assets/stylesheets/palette.06af60db.min.css | 1 + .../stylesheets/palette.06af60db.min.css.map | 1 + assets/ucdavis_logo_gold.png | Bin 0 -> 37600 bytes comparing-metagenomes/index.html | 878 +++ images/CD136-abundance.png | Bin 0 -> 34356 bytes images/CD136-venn.png | Bin 0 -> 23477 bytes images/CD136.amrfinder.png | Bin 0 -> 95323 bytes images/compare.abund.cmp.matrix.png | Bin 0 -> 34064 bytes images/compare.abund.mds.png | Bin 0 -> 14193 bytes images/compare.flat.cmp.matrix.png | Bin 0 -> 32783 bytes images/compare.flat.mds.png | Bin 0 -> 14323 bytes index.html | 632 ++ search/search_index.json | 1 + single-metagenomes-taxonomy/index.html | 981 +++ sitemap.xml | 3 + sitemap.xml.gz | Bin 0 -> 127 bytes 60 files changed, 11049 insertions(+) create mode 100644 .nojekyll create mode 100644 404.html create mode 100644 amr/index.html create mode 100644 assets/images/favicon.png create mode 100644 assets/javascripts/bundle.dd8806f2.min.js create mode 100644 assets/javascripts/bundle.dd8806f2.min.js.map create mode 100644 assets/javascripts/lunr/min/lunr.ar.min.js create mode 100644 assets/javascripts/lunr/min/lunr.da.min.js create mode 100644 assets/javascripts/lunr/min/lunr.de.min.js create mode 100644 assets/javascripts/lunr/min/lunr.du.min.js create mode 100644 assets/javascripts/lunr/min/lunr.el.min.js create mode 100644 assets/javascripts/lunr/min/lunr.es.min.js create mode 100644 assets/javascripts/lunr/min/lunr.fi.min.js create mode 100644 assets/javascripts/lunr/min/lunr.fr.min.js create mode 100644 assets/javascripts/lunr/min/lunr.he.min.js create mode 100644 assets/javascripts/lunr/min/lunr.hi.min.js create mode 100644 assets/javascripts/lunr/min/lunr.hu.min.js create mode 100644 assets/javascripts/lunr/min/lunr.hy.min.js create mode 100644 assets/javascripts/lunr/min/lunr.it.min.js create mode 100644 assets/javascripts/lunr/min/lunr.ja.min.js create mode 100644 assets/javascripts/lunr/min/lunr.jp.min.js create mode 100644 assets/javascripts/lunr/min/lunr.kn.min.js create mode 100644 assets/javascripts/lunr/min/lunr.ko.min.js create mode 100644 assets/javascripts/lunr/min/lunr.multi.min.js create mode 100644 assets/javascripts/lunr/min/lunr.nl.min.js create mode 100644 assets/javascripts/lunr/min/lunr.no.min.js create mode 100644 assets/javascripts/lunr/min/lunr.pt.min.js create mode 100644 assets/javascripts/lunr/min/lunr.ro.min.js create mode 100644 assets/javascripts/lunr/min/lunr.ru.min.js create mode 100644 assets/javascripts/lunr/min/lunr.sa.min.js create mode 100644 assets/javascripts/lunr/min/lunr.stemmer.support.min.js create mode 100644 assets/javascripts/lunr/min/lunr.sv.min.js create mode 100644 assets/javascripts/lunr/min/lunr.ta.min.js create mode 100644 assets/javascripts/lunr/min/lunr.te.min.js create mode 100644 assets/javascripts/lunr/min/lunr.th.min.js create mode 100644 assets/javascripts/lunr/min/lunr.tr.min.js create mode 100644 assets/javascripts/lunr/min/lunr.vi.min.js create mode 100644 assets/javascripts/lunr/min/lunr.zh.min.js create mode 100644 assets/javascripts/lunr/tinyseg.js create mode 100644 assets/javascripts/lunr/wordcut.js create mode 100644 assets/javascripts/workers/search.b8dbb3d2.min.js create mode 100644 assets/javascripts/workers/search.b8dbb3d2.min.js.map create mode 100644 assets/stylesheets/main.66ac8b77.min.css create mode 100644 assets/stylesheets/main.66ac8b77.min.css.map create mode 100644 assets/stylesheets/palette.06af60db.min.css create mode 100644 assets/stylesheets/palette.06af60db.min.css.map create mode 100644 assets/ucdavis_logo_gold.png create mode 100644 comparing-metagenomes/index.html create mode 100644 images/CD136-abundance.png create mode 100644 images/CD136-venn.png create mode 100644 images/CD136.amrfinder.png create mode 100644 images/compare.abund.cmp.matrix.png create mode 100644 images/compare.abund.mds.png create mode 100644 images/compare.flat.cmp.matrix.png create mode 100644 images/compare.flat.mds.png create mode 100644 index.html create mode 100644 search/search_index.json create mode 100644 single-metagenomes-taxonomy/index.html create mode 100644 sitemap.xml create mode 100644 sitemap.xml.gz diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/404.html b/404.html new file mode 100644 index 0000000..207650f --- /dev/null +++ b/404.html @@ -0,0 +1,511 @@ + + + +
+ + + + + + + + + + + + + + +We're going to use +AMRFinderPlus, +together with the +megahit metagenome assembler and +the +prodigal gene finder, +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.
+First, install the software. Run: +
mamba create -n amrfinder -y ncbi-amrfinderplus megahit prodigal csvtk matplotlib seaborn pandas
+conda activate amrfinder
+
Next, download the amrfinderplus database. Run: +
+And, finally, set up & change to a working directory. Run: +
+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, 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: +
megahit -1 ../data/IBD_tutorial_subset/metag/1-trimmed/CD136/CD136.1.paired.fq.gz \
+ -2 ../data/IBD_tutorial_subset/metag/1-trimmed/CD136/CD136.2.paired.fq.gz \
+ -o CD136.assembly.d
+
CD136.assembly.d/final.contigs.fa
.
+Now, predict proteins in the assembled contigs using prodigal: +
+This will produce a FASTA file containing many protein sequences: +
+These are the (partial & complete) genes found by theprodigal
software.
+And, finally, run AMRfinder on the proteins: +
+(This will take under a minute.) +AMRfinder will produce a spreadsheet named CD136.amrfinder.tsv
that
+contains a number of columns - you can see the list like so, using
+csvtk headers
:
To pick out just a few columns, you can use csvtk cut
.
Run: +
+and you will see: +
% Coverage of reference sequence HMM description
+89.41 CfxA family broad-spectrum class A beta-lactamase
+87.59 23S ribosomal RNA methyltransferase Erm
+52.84 NA
+100.00 macrolide efflux MFS transporter Mef(En2)
+100.00 lincosamide nucleotidyltransferase Lnu(AN2)
+100.00 CepA family extended-spectrum class A beta-lactamase
+
The first column here is the amount of the known (reference) sequence +that is present in the metagenome, and the second is the description of +the match.
+Note: If you wanted to get the abundance of these in the metagenome, +you would have to find the DNA contig that the relevant gene was on, +using the column "Protein identifier", and then map the metagenome +reads to it to get the abundance. This is because assembly collapses +the abundance of the output contigs, and you have to recover it through +other means.
+Now we can plot the abundances of the AMRs we found: +
+ + + + + + + + + + + + + + + + + + + + + + + +