[{"_1":2,"_161":-5,"_162":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_140":141},"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,"_129":-5,"_130":11,"_131":21,"_132":11,"_133":-5,"_134":11,"_135":-5,"_136":137,"_138":91,"_139":-7},"canonicalUrl","https://hub.docker.com/r/jkimlab/plrgen/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","jkimlab","reponame","plrgen","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","2022-03-02T07:51:06.126712Z","description","Tool for the generation of pseudo-long-reads","is_private","last_updated","2022-03-10T05:30:38.010156Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",815,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# Overview\n\nPLR-GEN is a tool for the generation of pseudo-long-reads (PLRs) by using short-reads of a metagenomic sample and microbial reference genome sequences as input. \n\nYou can see [PLR-GEN Github](https://github.com/jkimlab/PLR-GEN)\n\n## USAGE \n### Input preparation \n1. Input single-end or paired-end NGS short reads\n - Read sequence files are mandatory with fastq format (or compressed by .gz file)\n - You can use single-end reads with `-s` (incompatible with `-1` and `-2`)\n - Or you can use paired-end reads with `-1` and `-2` (incompatible with `-s`)\n\n2. A list of reference genome sequences\n - Reference genome sequence files are mendatory with fasta format (or compressed by .gz file)\n - You can use `-r` or `-ref` option (incompatible with `-tama`)with a list of all the file paths of reference genomes to set up the references for running PLR-GEN\n\n3. (Additional) If TAMA is installed, you can predict putative bacterial species in your dataset using TAMA, running PLR-GEN using `-tama` option (incompatible with `-r`). \n\n### Running options of PLR-GEN\n\n* Running PLR-GEN\n\n\t\tPLR-GEN.pl [options] -1 -2 (or -s ) -r -o \n\t\t\n\n1. Input options \n\n - `-s` : an input sequence file with unpaired reads (single-end reads); a fastq or fastq.gz file\n - `-1` and `-2` : input sequence files with paired-end reads; fastq or fastq.gz files \n - `-r` or `-ref` : a list with all file paths of reference genome sequences; a text file\n - `-tama` : if this option is used, TAMA program will be used for reference preparation instead of `-r` (default: not used)\n - `-sampling` : if this option is used, reference genomes will be randomly selected and used (default: not used)\n\n2. Output options \n\n - `-o` : a path of output directory (default: ./PR_out; final output: ./PR_out/pseudo-long-read.fa)\n - `-t` : if this option is used, all intermediated output files are saved (default: not used)\n\n3. Running options\n - `-p` : the number of threads\n - `-l` or `-min_length` : minimum length cutoff of generated pseudo-long reads (PLRs) (default: 100)\n - `-q` or `-mapq` : cutoff of mapping quality (used in samtools) (default: 20)\n - `-c` or `-min_count` : cutoff of mapping depth for generating normal nodes and bubbles; after piling-up of read mapping, alignment column less than the cutoff value will be discarded (default: 1)\n - `-d` or `-min_depth` : cutoff of mapping depth of bubbles for filtering bubble nodes; a bubble with less than the cutoff % of mapping depth will be converted to a normal node\n\n* Help page of PLR-GEN \n\n\t\tUsage: PLR-GEN.pl [options] -1 -2 (or -s ) -r -o \n\n\t\t== MANDATORY \n\t\t-s\t\tFile with unpaired reads [incompatible with -1 and -2]\n\t\t-1\t\tFile with #1 mates (paired 1) [incompatible with -s]\n\t\t-2\t\tFile with #2 mates (paired 2) [incompatible with -s]\n\t\t-r|-ref\t\tThe list of reference genome sequence files\n\t\t-tama\tReference preparation using TAMA [incompatible with -r|-ref]\n\t\t-sampling\t\tproportion to random sampling for references (default: off, range: 0-1)\n\t\t-o\t\tOutput directory (default: ./PR.out)\n\n\t\t==Running and filtering options\n\t\t-p|-core\t\tThe number of threads (default: 1)\n\t\t-q|-mapq\t\tMinimum mapping quality (default: 20)\n\t\t-l|-min_length\t\tCutoff of minimum length of pseudo-long reads (default: 100bp)\n\t\t-c|-min_count\t\tCutoff of minimum mapping depth for each node (default: 1)\n\t\t-d|-min_depth\t Cutoff of mapping depth of bubbles (default: 1, range: 0-100)\n\t\t\t\t0: all bubbles are used.\n\t\t\t\t1: bubbles with less than 1% mapping depth from mapping depth distribution of bubbles are converted to normal nodes.\n\t\t\t\t100: all bubbles are converted to normal nodes\n\n\t\t==Other options\n\t\t-t|-temp\tIf you use -t option, all intermediate files are left.\n\t\t\tPlease careful to use this option because it has to be needed very large space.\n\t\t-h|-help\tPrint help page.\n\n### (Additional) TAMA installation\n\n- For running PLR-GEN, if you want to use TAMA with `-tama` option for preparation of reference genomes, you can install TAMA using below commands. It will automatically download and install TAMA into the given path, and set ready-made species-level TAMA databases. These TAMA databases require total 300GB disk space, so please carefully set up the path for installation of TAMA. If you do not specify a path for TAMA, the TAMA package and TAMA databases will be set inside \"bin\" directory in the PLR-GEN. \n\n1. Installation of TAMA with Docker\n\n\t\tdocker run --rm -v /PATH/TO/TAMA_DIR:/tama_dir -t jkimlab/plrgen:latest /work_dir/src/TAMA_install.pl /tama_dir\n\t\t\n2. Manual installation\n\n- You can use manually installed TAMA. To use `-tama` option for PLR-GEN, you need to install TAMA and ready-made species-level databases into /LOCAL_DISK/PLR-GEN/bin/ directory or make a link of path of installed TAMA directory to /LOCAL_DISK/PLR-GEN/bin/ directory.\n\nFor more information of TAMA, see [TAMA Github](https://github.com/jkimlab/TAMA)\n\n\n### Examples of running PLR-GEN\n\n- Suppose (1) you pulled the PLR-GEN docker image (jkimlab/plrgen), (2) read_1.fq, read_2.fq are in /LOCAL_DISK/DATA directory, and (3) all reference sequence files are in /LOCAL_DISK/DATA/fasta/ directory. In this situation, you can run PLR-GEN with docker image as followed command,\n\t1. Make a reference list file in the /LOCAL_DISK/DATA directory with the file system for the docker image, for an example,\n\t\t\n\t\tfile: /DATA/reference_list.txt\n\t\t\n\t\t\t/data_dir/fasta/REF_1.fa\n\t\t\t/data_dir/fasta/REF_2.fa\n\t\t\t/data_dir/fasta/REF_3.fa\n\n\t2. Run the docker image, mounting /DATA directory to /data_dir directory of docker image, for an example,\n\n\t\t\tdocker run -v /LOCAL_DISK/DATA:/data_dir -t jkimlab/plrgen PLR-GEN.pl -1 /data_dir/read_1.fq -2 /data_dir/read_2.fq -r /data_dir/reference_list.txt -o /data_dir/output\n\t\t\t\n- If you want to use TAMA installed at /LOCAL_DISK/PROGRAMS/TAMA, you need to mount the TAMA directory to /work_dir/bin/ directory of docker image, for an example, \n\n\t\tdocker run -v /LOCAL_DISK/PROGRAMS/TAMA:/work_dir/bin/TAMA -v /LOCAL_DISK/DATA:/data_dir -t jkimlab/plrgen PLR-GEN.pl -1 /data_dir/read_1.fq -2 /data_dir/read_2.fq -r /data_dir/reference_list.txt -o /data_dir/output\n\n","has_starred","hub_user","immutable_tags_settings",{"_75":11,"_76":77},"enabled","rules",[78],".*","is_automated","permissions",{"_82":21,"_83":11,"_84":11},"read","write","admin","user","storage_size",2173165878,"orgData","recentTags",[91],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":100,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":66,"_128":21},"content_type","creator",15393424,"full_size",1074609273,"id",195082807,"images",[101],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":66,"_117":-5},"architecture","amd64","digest","sha256:a7c0a38dd0c9c293f2e3dec05b5de905f199c9ba3f5ecc377a52f035fc1b2e85","features","","last_pulled","2026-10-02T10:47:59.291741477Z","last_pushed","2022-03-10T05:30:38Z","os","linux","os_features","os_version","size","variant","2022-03-10T05:30:37.868495Z","last_updater","last_updater_username","media_type","latest","repository",16578663,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":142,"_149":150,"_136":159,"_160":11},{"_40":143,"_42":144,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":145,"_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":146,"_79":11,"_80":148,"_85":33,"_86":87},[],[44],[56],{"_75":11,"_76":147},[78],{"_82":21,"_83":11,"_84":11},"tags",{"_151":64,"_152":-5,"_153":-5,"_154":155},"count","next","previous","results",[156],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":157,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":66,"_128":21},[158],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":66,"_117":-5},[],"canDeleteTags","actionData","errors"]

jkimlab/plrgen

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