[{"_1":2,"_160":-5,"_161":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_139":140},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_88":-5,"_89":90,"_128":-5,"_129":11,"_130":21,"_131":11,"_132":-5,"_133":11,"_134":-5,"_135":136,"_137":91,"_138":-7},"canonicalUrl","https://hub.docker.com/r/jkimlab/rbrc/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","jkimlab","reponame","rbrc","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":74,"_79":11,"_80":81,"_85":33,"_86":87},"categories",[],"content_types",[44],"image","date_registered","2022-08-09T12:52:23.553808Z","description","","is_private","last_updated","2022-08-09T12:55:56.206486Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",752,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# OVERVIEW\n\nRBRC is a tool for NGS paired-end read clustering and de novo assembly based on Reference genome sequence-based read clustering\n\n## INSTALLATION\n\n docker pull jkimlab/rbrc\n\n## RUNNING RBRC\n\n1. Prepare `reference` directory with all reference sequence files and `read` directory with all paired-end fastq files.\n2. Make `output` directory.\n3. Prepare `params.txt` file as follows into the `output` directory\n\n #---------------------------------------------------------------------------------------#\n ## Mendatory !\n # Reference genomes\n REF\t1\t /rbrc_wd/reference/\n REF\t2\t /rbrc_wd/reference/\n\n # NGS reads\n # FASTQ\n >LIB1\n /rbrc_wd/read/\n /rbrc_wd/read/\n\n #---------------------------------------------------------------------------------------#\n ## Optional\n # Running paramters\n THREADS \n REF_SIMILARITY_CUTOFF \n MAPQ \n\n # Pairwise alignment & synteny block construction params\n RESOLUTION\t\n\n # Distance based clustering paramters\n DBC_READ_DIST_CUTOFF\t\n\n # Cluster merging parameter\n MERGE_MIN_READS\t\n #---------------------------------------------------------------------------------------#\n\n4. Run RBRC with follow command\n\n docker run -v /LOCALDISK/reference:/rbrc_wd/reference -v /LOCALDISK/read:/rbrc_wd/read -v /LOCALDISK/output:rbrc_wd/output -t rbrc:latest RBRC.pl -p /rbrc_wd/output/params.txt -o /rbrc_wd/output\n\n## RBRC output\n1. Clustering output\n\n output_directory/RBRC.cluster : list of cluster and clustered reads\n - Column 1: name of cluster\n - Column 2: Read ID\n \n [example]\n CLUSTER1\tchr8-278460/1\n CLUSTER1\tchr8-278460/2\n CLUSTER1\tchr8-278414/1\n CLUSTER1\tchr8-278414/2\n CLUSTER1\tchr8-278396/1\n CLUSTER1\tchr8-278396/2\n CLUSTER1\tchr8-278392/1\n CLUSTER1\tchr8-278392/2\n CLUSTER1\tchr8-278382/1\n CLUSTER1\tchr8-278382/2\n \n\n2. 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jkimlab/rbrc

Tags for jkimlab/rbrc