args_oap
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xinehc
ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
Hi everyone! I'm trying to run args_oap using a custom database (PlasmidFinder). I downloaded the db and indexed the .fasta file using: `args_oap make_db -i ~/path/to/db/plasmid_db.fasta` Now I'm trying to...
I see that this package uses the GreenGenes database of 16S rRNA genes. Depending on which version you're using, this database is potentially outdated. Could you let me know which...
Hello developer, thanks for this awesome tool, after running stage_two I got several output tables. Apparently args_oap produces ARGs count tables with different normalization methods am I right ? (rpkm,...
Hi! First of all, thanks for this tool! I've been using the normalized tables so far so I have never really paid attention to the unnormalized files but now I'm...
Hi, I am using the version 3.2.2 of args-oap on paired-end shotgun sequencing files. As mentioned "If you use paired-end files, please make sure the forward/reverse reads end with _1...
Dear Dr. Chen I have a question about the stage_two, could I set the parameters by myself, such as -l [length] -e [evalue] -d [identity]? best reagrds!
Hello I uploaded my fasta and metadata.txt files into the online pipeline v 2.2 The process completed in one second, i am not able to download my data when i...
Sorry, I couldn't open the online URL. http://smile.hku.hk/SARGs
I saw the newly published literature (https://www.sciencedirect.com/science/article/pii/S2095809922008062), but I can't the appendix on this website, and also the online pipeline website can't be opened.
When I run args_oap stage_one -i */arg_fasta/ -o */MGE_one/ -f fa -t 40 I got Processing (1/2) ... Traceback (most recent call last): File "*/miniconda3/envs/args_oap/bin/args_oap", line 10, in sys.exit(main()) ^^^^^^...
