shinejh0528/rgi repository overview

RGI Resistance Gene Identifier
RGI can be used to predict resistomes from protein or nucleotide data based on homology and SNP models. Analyses can be performed via this web portal (20 Mb limit), via the command line, or via use of a Galaxy wrapper. The command line version can be obtained from the Download section of the CARD website. You can additionally install RGI from Conda or run RGI from Docker.

This web portal supports analysis of genomes, genome assemblies, metagenomic contigs, or proteomes. The command line tool additionally supports analysis of metagenomic reads and k-mer prediction of pathogen-of-origin for AMR genes.

Web portal - RGI 6.0.2, CARD 3.2.7: Open Reading Frame (ORF) prediction using Prodigal, homolog detection using DIAMOND, and Strict significance based on CARD curated bitscore cut-offs. Options included for percent identity filtering, low quality/coverage assemblies, merged metagenomic reads, small plasmids or assembly contigs (<20,000 bp).

Online RGI results cached for 7 days. As the CARD curation evolves, the results of the RGI evolve. RGI targets, reference sequences, and significance cut-offs are under constant curation. Full documentation for the RGI can be found at GitHub.

>2_1188 | model_type_id: 40292 | pass_bitscore: 575 | CblA-1
MKAYFIAILTLFTCIATVVRAQQMSELENRIDSLLNGKKATVGIAVWTDKGDMLRYNDHVHFPLLSVFKFHVALAVLDKMDKQSISLDSIVSIKASQMPPNTYSPLRKKFPDQDFTITLRELMQYSISQSDNNACDILIEYAGGIKHINDYIHRLSIDSFNLSETEDGMHSSFEAVYRNWSTPSAMVRLLRTADEKELFSNKELKDFLWQTMIDTETGANKLKGMLPAKTVVGHKTGSSDRNADGMKTADNDAGLVILPDGRKYYIAAFVMDSYETDEDNANIIARISRMVYDAMR
>4_1393 | model_type_id: 40292 | pass_bitscore: 550 | SHV-52
MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLAIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR
>5_677 | model_type_id: 40292 | pass_bitscore: 300 | dfrF
MIGLIVARSKNNVIGKNGNIPWKIKGEQKQFRELTTGNVVIMGRKSYEEIGHPLPNRMNIVVSTTTEYQGDNLVSVKSLEDALLLAKGRDVYISGGYGLFKEALQIVDKMYITEVDLNIEDGDTFFPEFDINDFEVLIGETLGEEVKYTRTFYVRKNELSRFWI
>7_1703 | model_type_id: 40292 | pass_bitscore: 500 | CTX-M-130
MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRHDVLASAARIIAEGL
>8_1103 | model_type_id: 40292 | pass_bitscore: 500 | NDM-6
MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASVRAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

rgi main --input_sequence proteindb.fsa --output_file test --local --clean --input_type protein

docker run -v /TBI:/TBI shinejh0528/rgi:1.0.0 /bin/bash -c "rgi main --input_sequence /TBI/People/tbi/jhshin/script/docker/rgi/test/proteindb.fsa --output_file /TBI/People/tbi/jhshin/script/docker/rgi/test/test --local --clean --input_type protein && chown -R jhshin:bioinfo /TBI/People/tbi/jhshin/script/docker/rgi/test"

# run (just execute command)
singularity run -H$PWD --bind /TBI docker://shinejh0528/rgi:1.0.1 [command]

# exec (connect to shell)
singularity exec -H$PWD --bind /TBI docker://shinejh0528/rgi:1.0.1 /bin/bash