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+ + + + + + + + + + + + + + +@CTB links to software
+ +Download the amrfinder database: +
+and set up & change to a working directory: +
+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.
+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: +
+And, finally, run AMRfinder on the proteins: +
+ +@CTB examine output files.
+ + + + + + + + + + + + + + + + + + + + + + +