diff --git a/_sources/about.rst.txt b/_sources/about.rst.txt index 229befb..86f016c 100644 --- a/_sources/about.rst.txt +++ b/_sources/about.rst.txt @@ -24,7 +24,7 @@ About Master of Pores 3 - |nver| - |sing| -`Master of Pores 3`_ is a collection of pipelines written in Nextflow DSL2 for the analysis of Nanopore data. It can handle reads from direct RNAseq, cDNAseq, DNAseq etc. +`Master of Pores 3 `_ is a collection of pipelines written in Nextflow DSL2 for the analysis of Nanopore data. It can handle reads from direct RNAseq, cDNAseq, DNAseq etc. The software is composed by four pipelines: diff --git a/about.html b/about.html index 1283761..794f65a 100644 --- a/about.html +++ b/about.html @@ -106,7 +106,7 @@ -

`Master of Pores 3`<https://github.com/biocorecrg/master_of_pores>_ is a collection of pipelines written in Nextflow DSL2 for the analysis of Nanopore data. It can handle reads from direct RNAseq, cDNAseq, DNAseq etc.

+

Master of Pores 3 is a collection of pipelines written in Nextflow DSL2 for the analysis of Nanopore data. It can handle reads from direct RNAseq, cDNAseq, DNAseq etc.

The software is composed by four pipelines:

    diff --git a/searchindex.js b/searchindex.js index 7ff3071..43e7527 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"About Master of Pores 3": [[0, null]], "Barcodes": [[8, "barcodes"]], "Basecalling with the m6A-aware model": [[8, "basecalling-with-the-m6a-aware-model"]], "Benchmark": [[1, null]], "CHANGELOG": [[2, null]], "Continuous integration": [[3, null]], "Dataset": [[1, "id1"]], "Demultiplexing with Guppy": [[11, "demultiplexing-with-guppy"]], "Encoding of modification information from m6A-aware basecalled data using modPhred": [[7, "encoding-of-modification-information-from-m6a-aware-basecalled-data-using-modphred"]], "Get Started": [[5, null]], "How to run the pipeline": [[6, "how-to-run-the-pipeline"], [7, "how-to-run-the-pipeline"], [8, "how-to-run-the-pipeline"], [9, "how-to-run-the-pipeline"]], "Html report": [[10, "html-report"]], "Input Parameters": [[6, "input-parameters"], [7, "input-parameters"], [8, "input-parameters"], [9, "input-parameters"]], "Installing Guppy": [[5, "installing-guppy"]], "Live reporting": [[10, "live-reporting"]], "MOP_CONSENSUS": [[6, null]], "MOP_MOD": [[7, null]], "MOP_PREPROCESS": [[8, null]], "MOP_TAIL": [[9, null]], "Memory failures in mop_preprocess and mop_mod": [[11, "memory-failures-in-mop-preprocess-and-mop-mod"]], "Model libraries for specific tools": [[8, "model-libraries-for-specific-tools"]], "Profiles": [[5, "profiles"]], "Reference": [[0, "reference"]], "Resource reporting": [[10, null]], "Results": [[6, "results"], [7, "results"], [8, "results"], [9, "results"]], "Testing": [[5, "testing"]], "Troubleshooting": [[11, null]], "Version 1.0": [[2, "version-1-0"]], "Version 1.1": [[2, "version-1-1"]], "Version 2.0": [[2, "version-2-0"]], "Version 3.0": [[2, "version-3-0"]], "Welcome to the documentation of Master Of Pores 3": [[4, null]], "tool_opts": [[8, "tool-opts"]]}, "docnames": ["about", "benchmark", "changelog", "ci", "index", "install", "mop_consensus", "mop_mod", "mop_preprocess", "mop_tail", "reporting", "troubleshooting"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about.rst", "benchmark.rst", "changelog.rst", "ci.rst", "index.rst", "install.rst", "mop_consensus.rst", "mop_mod.rst", "mop_preprocess.rst", "mop_tail.rst", "reporting.rst", "troubleshooting.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [0, 1, 5, 7, 8, 11], "0": [5, 7, 8, 11], "0000": 7, "00000": 7, "0014": 7, "0027": 7, "004": 7, "01119f62": 9, "013a5dd": 9, "0154ce9c": 9, "020cde28": 9, "03": 7, "030": 8, "039": 8, "04250": 7, "05": 9, "06": 11, "06165301236574491": 7, "0716": 0, "07733386075949367": 7, "0822032221904741": 7, "09386043857145993": 7, "0997da": 8, "1": [0, 5, 7, 8], "10": [0, 1, 11], "100": [1, 11], "1007": 0, "102": 7, "104": 7, "10802503018992206": 7, "10855198155670216": 7, "11": 5, "113": 7, "115": 7, "13": 1, "13540820136616222": 7, "137": 1, "14": 1, "14792457800118533": 7, "1505633771881658": 7, "159196780": 11, "16": 9, "17": [0, 5], "17128164556962025": 7, "185": 0, "18715519704595907": 7, "1_70bps_m6a_hac": 8, "2": [1, 5, 7, 8], "20": 11, "2020": 0, "2023": 0, "2033057488421099": 7, "2034": 7, "20497099156118143": 7, "205": 0, "2058377475437941": 7, "2080": 1, "2082775277198375": 7, "231": 9, "24": [7, 9, 11], "25": [1, 7], "2515": [7, 11], "2516": 7, "2517": 7, "2518": 7, "2519": 7, "2624": 0, "27": 9, "274": 9, "28": 9, "2962": 0, "3": [1, 5, 7], "30": 11, "315": 7, "32995": 11, "33": [2, 8], "35": 7, "36995": 7, "382": 1, "38207": 7, "39": 9, "4": [2, 5, 7, 8, 11], "40": 11, "4000": 8, "41": 9, "416": 7, "422": 7, "433": 7, "45497": 7, "45504": 7, "45529": 7, "45545": 7, "45557": 7, "458d": 9, "471": 7, "4710": 9, "47485": 7, "49": 9, "49821": 7, "4de1": 9, "4ebc": 9, "5": [1, 2, 5, 7, 8], "50": [6, 11], "506": 7, "51247": 7, "517fdc524207": 9, "52": 9, "56": 9, "595": 1, "6": [1, 2, 5, 7, 8], "60": 11, "6353d6": 8, "64": 9, "7": 7, "70": [7, 11], "71619": 7, "76": 1, "79": 9, "8": [1, 7], "80": 11, "81853": 7, "82488e": 11, "82eeaa": 8, "83eb": 9, "87": 7, "88": 7, "89": 7, "8_13": 0, "90": 11, "90a5": 9, "92": 7, "92130": 7, "93": 7, "95": [1, 7], "97": 7, "970d": 9, "97797": 7, "977e4b4bbc46": 9, "978": 0, "9c52": 9, "9d": 8, "A": [0, 2, 7, 9], "For": [2, 5, 8, 10], "If": [0, 2, 8, 9], "In": 8, "It": [0, 2, 4, 5, 6, 7, 8, 9, 11], "NO": [2, 7], "No": [2, 11], "Not": 2, "Of": 0, "One": 8, "The": [0, 1, 2, 3, 4, 6, 7, 8, 9], "Then": [8, 10], "To": [5, 6, 7, 8, 9], "_": 0, "_opt": 2, "_out": 11, "aa1f": 9, "aaatt": 7, "aattg": 7, "about": [4, 10], "absolut": 8, "accept": 2, "access": [1, 10], "accordingli": [2, 8], "act": 2, "action": 3, "actrun_newdata_nanopore_uresnet20v2_model": 8, "ad": [2, 6, 7, 8, 9, 10], "add": [2, 8, 10], "addit": 9, "affect": 8, "after": 8, "algorithm": 7, "align": [0, 2, 7, 8, 9], "all": 6, "allow": 2, "alreadi": [2, 8], "also": [2, 8], "alwai": 11, "amazon": 5, "among": [2, 5], "amount": 2, "an": [2, 5, 6, 7, 8, 9, 10], "analysi": [0, 2, 4, 7, 8], "ani": [8, 11], "anna": [0, 8], "anno": [7, 9], "anoth": [7, 8], "appl": [5, 8], "ar": [2, 3, 5, 6, 7, 8, 9], "assembl": 8, "assembli": 8, "assign": [8, 9], "attga": 7, "authent": 10, "automat": [2, 5, 8], "avail": 8, "aw": [2, 5], "awsbatch": [2, 5], "ax": 8, "b5": 8, "b8d053": 8, "back": 10, "background": [6, 7, 8, 9], "bam": 8, "bambu": [2, 8], "barcod": [2, 11], "barcode01": 8, "barcode02": 8, "barcode_kit": 11, "barcodeid": 8, "base": [7, 8, 10], "basecal": [0, 2, 5, 9, 11], "basecallnew": 8, "basenam": 8, "bash": 5, "bash_profil": 10, "bashrc": 10, "batch": [2, 8], "bbb1": 9, "bc_1": 8, "bc_102": 8, "bc_104": 8, "bc_2": 8, "bc_3": 8, "becaus": 11, "bed": 2, "been": [7, 8], "befor": [5, 6, 7, 8, 9], "begin": 8, "being": [2, 5], "below": 7, "benchmark": 4, "beta": 2, "between": 0, "bg": [5, 6, 7, 8, 9, 10], "bin": 2, "biocor": 5, "biocorecrg": [0, 5], "bioinformat": 0, "biol": 0, "bionextflow": 2, "both": [6, 7, 8, 9], "broken": 2, "bwa": 8, "c": [7, 8], "ca68": 9, "cach": 8, "call": [2, 8, 11], "caller": 11, "can": [0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11], "cannot": [8, 11], "card": 1, "case": 8, "cd": [5, 7, 8], "cdna": 2, "cdnaseq": [0, 4], "cf8c8c04cd3b": 9, "cfg": 8, "chang": [6, 7, 8, 9], "changelog": 4, "check": [3, 8, 11], "checkref": 8, "chemic": [0, 4], "chemistri": [2, 9], "chr": 7, "ci": 5, "cite": 0, "clone": 5, "cloud": [2, 5], "cluster": [2, 5, 8], "code": 7, "collect": 0, "column": 8, "com": [0, 2, 5], "combin": 9, "come": 2, "command": [2, 6, 7, 8, 9, 11], "comparison": [6, 7], "compat": 5, "compil": 8, "complet": [2, 11], "compore_flow": 7, "compos": [0, 4], "comprehens": 10, "compress": [2, 5], "conf": 5, "config": [2, 6, 7, 8, 9], "configur": 5, "consensu": [0, 4, 6], "consid": 5, "contain": [5, 6, 7, 8, 9, 11], "content": 4, "contig": 7, "continu": [4, 5], "control": 8, "convent": 8, "convers": 2, "copi": 8, "core": 0, "correl": 9, "correspond": 8, "count": [0, 2, 8], "cov": 7, "coverag": 7, "coverage_ivt": 7, "coverage_sampl": 7, "cozzuto": 0, "cpu": [1, 10], "cram": [2, 8], "cram_fil": 8, "creat": [7, 8, 9], "crg": [0, 1, 2, 5, 8], "cuda11": 2, "curl": 5, "current": [5, 7], "custom": [2, 5], "dash": 8, "data": [0, 1, 4, 11], "dataset": [0, 2], "db70fb2cd130": 9, "decid": [6, 7, 8, 9], "dedic": 8, "deeplexicon": [2, 8], "deeplexicon_model": 8, "default": [5, 7], "del": 7, "delgado": 0, "delimit": 7, "demultiplex": [0, 2, 8], "depth": 5, "detail": [7, 8], "detect": [0, 4, 7, 8], "develop": 10, "difer": 6, "differ": [2, 5, 6, 7, 8, 9], "direct": [0, 2, 4], "directli": [0, 4], "directori": [6, 7, 8, 9, 11], "discov": 2, "discoveri": [2, 8], "disk": [2, 10], "distribut": 10, "dna": 2, "dnaseq": [0, 4], "do": [2, 8], "docker": [5, 6, 7, 8, 9, 10], "doi": 0, "don": 8, "dorado": [2, 8], "dorado_model": 8, "doubl": 11, "down": [2, 8], "download": [5, 8], "downsampl": 2, "downstream": [7, 8], "drna": 2, "drna_tool_m6a_splice_opt": 8, "drna_tool_splice_m6a_opt": 2, "dsl2": [0, 2, 4], "dure": 5, "dynam": 0, "e": 9, "e5": 8, "e5c990": 8, "each": [1, 2, 6, 7, 8, 10], "edit": 8, "either": [2, 5, 6, 7, 8, 9, 10, 11], "em": 0, "email": [6, 7, 9], "embed": 10, "emul": [5, 8], "ena": 1, "enabl": 10, "engin": 5, "environ": [5, 8, 10], "environment": 10, "epinano": [2, 7, 11], "epinano_flow": 7, "epinano_plot": 7, "epitranscriptom": 0, "err": 8, "err5296640": 1, "err5303454": 1, "error": [2, 8, 11], "estim": [0, 4, 9], "etc": [0, 4, 5, 8], "eu": 5, "eva": 0, "eventalign": 7, "eventu": 11, "exampl": [2, 6, 7, 8, 9, 10, 11], "execut": [1, 2, 5, 8, 10], "executor": 8, "explain": 8, "explan": 7, "export": 10, "extra": [2, 8], "extract": 2, "extrapar": 8, "extraparam": 6, "f": 8, "f5": [5, 8], "fa": [6, 7, 8, 9], "fast5": [2, 5, 7, 8, 9], "fast5_fil": 8, "faster": 2, "fastq": [2, 7, 8, 9, 11], "fastq_fil": 8, "fastqc": 11, "fb": 8, "fe6b": 9, "featur": [7, 8], "feed": [6, 7, 8, 9], "file": [2, 5, 6, 7, 8, 9, 10, 11], "fill": [6, 7, 9], "filter": [2, 8, 11], "final": [8, 10], "final_summary_": 2, "fine": 2, "finish": [10, 11], "first": 8, "flo": 11, "flow": 7, "flowcel": [2, 11], "folder": [1, 5, 7, 8, 9], "follow": [3, 6, 7, 8, 9, 10], "format": [2, 8], "formerli": 2, "four": [0, 4, 6, 7], "frequenc": 7, "from": [0, 2, 4, 5, 6, 8, 9], "front": 0, "function": 10, "furthermor": 8, "gaaga": 7, "gb": 1, "geforc": 1, "gene": [8, 9], "gene_a": 7, "gene_a_3": 7, "gene_a_4": 7, "gene_a_5": 7, "gene_a_6": 7, "gene_a_7": 7, "gene_a_8": 7, "gener": [0, 2, 4, 7, 8, 9, 10], "genet": 0, "genom": 8, "get": [2, 4], "getvers": 8, "git": 5, "github": [0, 2, 3, 5, 10], "given": 8, "global": 2, "go": [8, 10], "good": [10, 11], "googl": 10, "gpu": [1, 2, 5], "graphmap": 8, "graphmap2": 8, "grid": 5, "group": 0, "guppi": [2, 8], "guppy65_basecal": 8, "guppy_vers": 8, "gz": [7, 8, 9], "gzip": 7, "h5": 8, "ha": [7, 8, 10], "had": 8, "handl": [0, 4], "have": [2, 5, 8, 10], "here": [6, 7, 8, 9, 10], "hermoso": 0, "hour": 1, "hpc": [1, 5, 8], "htseq": [2, 8], "http": [0, 2, 5, 10], "huanl": 0, "i": [0, 2, 4, 5, 7, 8, 9, 10, 11], "id": [8, 9], "idea": 11, "improv": 2, "includ": 7, "independ": 2, "indic": [2, 8, 11], "individu": 7, "info": 2, "inform": [8, 10], "infrastructur": 5, "init": 11, "input": [0, 1, 11], "input_path": [6, 7, 9], "ins": 7, "insid": [2, 5], "inspir": 0, "instal": [2, 8], "instanc": 8, "instead": 2, "integr": [4, 5], "interest": 8, "intermedi": 8, "internet": 10, "io": 5, "isoqu": 2, "issu": 2, "its": [7, 10], "j": 0, "java": 5, "job": 1, "joint": 0, "julia": 0, "just": [5, 8, 10], "k14": 8, "keep_barcod": 2, "kept": [2, 8], "kind": 8, "kit": [2, 11], "known": 2, "ko": 7, "ko_1": 7, "ko_2": 7, "l": 0, "lab": 10, "laptop": 5, "later": [5, 7], "launch": [2, 6, 7, 8, 9, 10], "length": 9, "leszek": 0, "level": [7, 9], "like": [6, 7, 8, 9], "limit": [2, 8], "line": [2, 6, 7, 8, 9, 10], "link": 2, "linux": 5, "list": 8, "liu": 0, "local": [2, 5, 8, 10], "log": [5, 6, 7, 8, 9, 10], "look": 10, "low": [5, 11], "lsk114": 11, "luca": 0, "m": [8, 11], "m1": [5, 8], "m1mac": [5, 8], "m2": 5, "m3": 5, "m6a": 2, "make": 2, "mantain": 10, "map": [2, 8], "march": 0, "maria": 0, "master_of_por": [0, 5], "masterofpor": [0, 2], "maximum": 1, "mb": 1, "medaka": 2, "median": 7, "memori": 10, "mer": 7, "merg": 2, "metallica": 0, "method": 0, "mi": 7, "min": 1, "min114": 11, "minimap2": [2, 8], "minion": 1, "mirror": 2, "mod": 8, "mode": [2, 9], "model": [2, 5, 7], "modelnam": 8, "modif": [0, 4], "modifi": 8, "modul": [2, 4, 7], "mol": 0, "mop": [1, 10], "mop2": 8, "mop3": 8, "mop3_pub": 5, "mop_consensu": [0, 1, 2, 4], "mop_mod": [0, 1, 2, 3, 4, 6], "mop_preprocess": [0, 1, 2, 3, 4, 5, 7, 9, 10], "mop_tail": [0, 1, 2, 3, 4], "more": [0, 7, 8], "multi": 8, "multifast5": 8, "multipl": 2, "multiqc": 8, "multithread": 2, "must": [8, 11], "myfil": 8, "n": 0, "n3ps_r10": [2, 9], "n3ps_r9": [2, 9], "na": 7, "name": [0, 8, 9], "nano3p": [2, 9], "nanocompor": 7, "nanoconsensu": 6, "nanocount": 8, "nanofilt": [8, 11], "nanomod": 2, "nanopolish": [7, 9], "nanopor": [0, 2, 4], "nanoporetech": 2, "nanopreprocess": 2, "nanopreprocesssimpl": 2, "nanoq": [8, 11], "nanoq_filt": 8, "nanotail": 2, "nbd114": 11, "need": [2, 5, 8], "netxtlow": 8, "new": [2, 8], "next": 8, "nextflow": [0, 2, 4, 5, 6, 7, 8, 9, 10], "nf": [5, 6, 7, 8, 9, 10], "nice": 10, "nm": 1, "novel": 8, "novoa": 0, "now": [2, 10], "number": 8, "o": 5, "obtain": 8, "off": 2, "old": 2, "onc": [7, 8, 10], "one": [2, 5, 6, 7, 8, 9], "ones": 2, "onli": [5, 8], "open": 11, "option": [2, 8], "origin": 2, "other": [2, 7, 8, 11], "otherwis": 8, "our": [0, 5, 7], "out": 11, "outfold": [7, 9], "output": [0, 1, 2, 4, 6, 7, 8, 9, 11], "output_mod": [6, 7], "outputpoli": 9, "oxford": [0, 2], "oxfordnanoport": 2, "p": [0, 7], "padsiz": 6, "pamp": 8, "paper": [0, 2], "parallel": [1, 2, 6], "param": [2, 5, 6, 7, 8, 9], "paramet": [2, 10], "pars_tool": [2, 7, 8, 9], "path": [2, 5, 6, 7, 8, 9], "peopl": 10, "per": [2, 7, 8, 11], "perform": [2, 7, 8], "pipelin": [0, 2, 3, 4, 5, 10], "place": [2, 5], "pleas": [0, 5, 6, 7, 8, 9], "plot": [2, 7, 9], "po": 7, "pod5": [2, 8], "poli": 9, "polya": [0, 4, 9], "polya_fin": 9, "ponomarenko": 0, "posit": 7, "posix": 5, "possibl": 2, "power": 2, "pre": [2, 8], "predict": [0, 4, 6, 7, 9], "prefer": 5, "preprocess": [0, 4], "present": 2, "prevent": 2, "previous": 8, "proce": 8, "process": [0, 2, 8, 10], "processor": [5, 8], "produc": 8, "profil": [2, 8, 10], "program": 9, "project": 0, "projectdir": [6, 7, 9], "protocol": 9, "provid": 9, "pryszcz": 0, "pu": 1, "public": 5, "publish": [1, 2], "pulido": 0, "puppet": 0, "q_mean": 7, "q_median": 7, "q_std": 7, "qc": 8, "qc_file": 8, "qualiti": [7, 8, 11], "quantifi": 2, "r10": [2, 9], "r9": [2, 9], "raw": [7, 8], "re": 8, "read": [0, 2, 4, 7, 8, 9, 11], "read_nam": 7, "readuck": [2, 8], "recommend": 10, "recurs": 5, "reduc": 2, "ref": 7, "ref_posit": 7, "refer": [6, 7, 8, 9], "reference_km": 7, "refin": 8, "remov": 11, "rep2": 8, "replac": 5, "repo": 5, "report": [4, 7, 8], "repositori": [2, 5, 7], "repres": [6, 7, 8, 9], "requir": [2, 5], "research": 0, "resnet20": 8, "resourc": [4, 5], "respect": [7, 8, 9], "rest": 8, "restrict": 8, "result": 2, "resum": [2, 8], "retriev": 2, "rewritten": 2, "right": 5, "rm": 11, "rna": [0, 2, 5, 7], "rna002_70bps_hac": 8, "rna_r9": 8, "rnaseq": [0, 4, 8], "row": 11, "rtx": 1, "run": [1, 2, 5, 10, 11], "sampl": [1, 7, 8, 11], "sample_processed_perpos_median": 7, "samplenam": 8, "savespac": 2, "schedul": 8, "section": 8, "see": [7, 8, 10], "select": [5, 8], "seq": 9, "seqera": 10, "seqfilt": 8, "sequenc": [0, 2, 8], "set": [2, 8], "sever": [7, 8, 9], "sge": [2, 5, 8], "sh": [2, 5], "should": [2, 6, 7, 8, 9, 10], "show": 9, "sinc": 10, "singl": 8, "singular": [5, 6, 7, 8, 9], "size": [0, 4, 9, 11], "slurm": [5, 8], "so": 8, "softwar": [0, 7], "solut": 11, "solv": 8, "some": [5, 8], "sometim": 11, "soon": 2, "space": 2, "special": 8, "specifi": [2, 6, 7, 8, 9], "splice": 8, "sqk": 11, "standard": [2, 9], "start": [2, 4, 8], "stat": 2, "step": [2, 7, 8], "store": [2, 5, 6, 7, 8, 9], "submit": 8, "submodul": 5, "subworkflow": 2, "successfulli": 11, "suggest": 10, "sum": 7, "sun": 5, "support": [2, 5, 8], "switch": [2, 5], "syntax": 2, "system": 5, "t": [0, 7, 8], "tab": 7, "tail": [0, 4, 9], "tailfind": 2, "tailfindr": [2, 9], "tailfindr_mod": [2, 9], "tailfinr": 9, "take": [6, 7, 8, 9], "tar": 5, "tejedor": 0, "temporari": [6, 7, 8, 9], "test": [1, 9], "test2": [6, 7, 8, 9], "text": 8, "tgaag": 7, "thank": 2, "thei": 8, "them": [5, 7, 8, 11], "thi": [0, 2, 6, 7, 8, 9, 10], "those": 2, "three": 9, "through": 5, "ti": 1, "time": [1, 2, 11], "togeth": [7, 9], "token": 10, "tombo": [2, 7], "tombo_flow": 7, "tombo_kmerscor": 7, "tombo_lsc": 7, "tombo_msc": 7, "tombo_sitescor": 7, "toni": 0, "too": 2, "tool": [0, 2, 6, 9, 11], "tool_opt": [2, 11], "tools_opt": [2, 6, 7, 9], "tower": 10, "tower_access_token": 10, "train1_newdata_nanopore_uresnet20v2_model": 8, "transcript": [2, 6, 7, 8, 9], "transcriptom": [7, 8], "trigger": 2, "troubleshoot": [4, 8], "tsv": [2, 6, 7, 8, 9], "ttgaa": 7, "tune": 2, "two": [1, 2, 7], "txt": [2, 6, 7, 8, 9], "uf": 8, "unsplic": 7, "up": [1, 5, 8, 11], "upgrad": 2, "us": [0, 1, 2, 3, 5, 6, 8, 9, 10, 11], "usag": 10, "user": [6, 7, 8, 9], "v3": 8, "valu": 7, "variabl": 10, "variant": 2, "vbz": [2, 5], "vbz_compress": 2, "version": [5, 8], "via": [2, 6, 7, 8, 9], "w": [6, 7, 8, 9], "wa": [1, 8], "want": [5, 8], "warm": 8, "warn": 2, "we": [1, 2, 5, 8, 10], "websit": 10, "well": [7, 8], "were": 8, "when": 2, "where": [1, 2], "which": [6, 7, 8, 9], "window": 5, "within": [5, 7, 8, 9], "without": 5, "won": 8, "work": [1, 6, 7, 8, 9], "workflow": [0, 2], "working_directori": [6, 7, 8, 9], "worklow": 6, "write": 8, "written": [0, 4], "wsl": 5, "wt": [7, 8], "wt_1": 7, "wt_1_vs_ko_1_nanocompore_result": 7, "wt_2": 7, "x": [2, 5, 8], "yaml": [5, 6, 7, 8, 9], "ydr133c": 9, "ye": [2, 7, 9], "yeast_rrna_ref": [7, 8, 9], "yet": 2, "yfl044c": 9, "ygl238w": 9, "ykr072c": 9, "you": [0, 2, 5, 6, 7, 8, 9, 10, 11], "your": [8, 10, 11], "yourdomain": 9, "yourlog": [7, 8], "yournam": 9}, "titles": ["About Master of Pores 3", "Benchmark", "CHANGELOG", "Continuous integration", "Welcome to the documentation of Master Of Pores 3", "Get Started", "MOP_CONSENSUS", "MOP_MOD", "MOP_PREPROCESS", "MOP_TAIL", "Resource reporting", "Troubleshooting"], "titleterms": {"0": 2, "1": 2, "2": 2, "3": [0, 2, 4], "Of": 4, "about": 0, "awar": [7, 8], "barcod": 8, "basecal": [7, 8], "benchmark": 1, "changelog": 2, "continu": 3, "data": 7, "dataset": 1, "demultiplex": 11, "document": 4, "encod": 7, "failur": 11, "from": 7, "get": 5, "guppi": [5, 11], "how": [6, 7, 8, 9], "html": 10, "inform": 7, "input": [6, 7, 8, 9], "instal": 5, "integr": 3, "librari": 8, "live": 10, "m6a": [7, 8], "master": [0, 4], "memori": 11, "model": 8, "modif": 7, "modphr": 7, "mop_consensu": 6, "mop_mod": [7, 11], "mop_preprocess": [8, 11], "mop_tail": 9, "paramet": [6, 7, 8, 9], "pipelin": [6, 7, 8, 9], "pore": [0, 4], "profil": 5, "refer": 0, "report": 10, "resourc": 10, "result": [6, 7, 8, 9], "run": [6, 7, 8, 9], "specif": 8, "start": 5, "test": 5, "tool": 8, "tool_opt": 8, "troubleshoot": 11, "us": 7, "version": 2, "welcom": 4}}) \ No newline at end of file +Search.setIndex({"alltitles": {"About Master of Pores 3": [[0, null]], "Barcodes": [[8, "barcodes"]], "Basecalling with the m6A-aware model": [[8, "basecalling-with-the-m6a-aware-model"]], "Benchmark": [[1, null]], "CHANGELOG": [[2, null]], "Continuous integration": [[3, null]], "Dataset": [[1, "id1"]], "Demultiplexing with Guppy": [[11, "demultiplexing-with-guppy"]], "Encoding of modification information from m6A-aware basecalled data using modPhred": [[7, "encoding-of-modification-information-from-m6a-aware-basecalled-data-using-modphred"]], "Get Started": [[5, null]], "How to run the pipeline": [[6, "how-to-run-the-pipeline"], [7, "how-to-run-the-pipeline"], [8, "how-to-run-the-pipeline"], [9, "how-to-run-the-pipeline"]], "Html report": [[10, "html-report"]], "Input Parameters": [[6, "input-parameters"], [7, "input-parameters"], [8, "input-parameters"], [9, "input-parameters"]], "Installing Guppy": [[5, "installing-guppy"]], "Live reporting": [[10, "live-reporting"]], "MOP_CONSENSUS": [[6, null]], "MOP_MOD": [[7, null]], "MOP_PREPROCESS": [[8, null]], "MOP_TAIL": [[9, null]], "Memory failures in mop_preprocess and mop_mod": [[11, "memory-failures-in-mop-preprocess-and-mop-mod"]], "Model libraries for specific tools": [[8, "model-libraries-for-specific-tools"]], "Profiles": [[5, "profiles"]], "Reference": [[0, "reference"]], "Resource reporting": [[10, null]], "Results": [[6, "results"], [7, "results"], [8, "results"], [9, "results"]], "Testing": [[5, "testing"]], "Troubleshooting": [[11, null]], "Version 1.0": [[2, "version-1-0"]], "Version 1.1": [[2, "version-1-1"]], "Version 2.0": [[2, "version-2-0"]], "Version 3.0": [[2, "version-3-0"]], "Welcome to the documentation of Master Of Pores 3": [[4, null]], "tool_opts": [[8, "tool-opts"]]}, "docnames": ["about", "benchmark", "changelog", "ci", "index", "install", "mop_consensus", "mop_mod", "mop_preprocess", "mop_tail", "reporting", "troubleshooting"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about.rst", "benchmark.rst", "changelog.rst", "ci.rst", "index.rst", "install.rst", "mop_consensus.rst", "mop_mod.rst", "mop_preprocess.rst", "mop_tail.rst", "reporting.rst", "troubleshooting.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [0, 1, 5, 7, 8, 11], "0": [5, 7, 8, 11], "0000": 7, "00000": 7, "0014": 7, "0027": 7, "004": 7, "01119f62": 9, "013a5dd": 9, "0154ce9c": 9, "020cde28": 9, "03": 7, "030": 8, "039": 8, "04250": 7, "05": 9, "06": 11, "06165301236574491": 7, "0716": 0, "07733386075949367": 7, "0822032221904741": 7, "09386043857145993": 7, "0997da": 8, "1": [0, 5, 7, 8], "10": [0, 1, 11], "100": [1, 11], "1007": 0, "102": 7, "104": 7, "10802503018992206": 7, "10855198155670216": 7, "11": 5, "113": 7, "115": 7, "13": 1, "13540820136616222": 7, "137": 1, "14": 1, "14792457800118533": 7, "1505633771881658": 7, "159196780": 11, "16": 9, "17": [0, 5], "17128164556962025": 7, "185": 0, "18715519704595907": 7, "1_70bps_m6a_hac": 8, "2": [1, 5, 7, 8], "20": 11, "2020": 0, "2023": 0, "2033057488421099": 7, "2034": 7, "20497099156118143": 7, "205": 0, "2058377475437941": 7, "2080": 1, "2082775277198375": 7, "231": 9, "24": [7, 9, 11], "25": [1, 7], "2515": [7, 11], "2516": 7, "2517": 7, "2518": 7, "2519": 7, "2624": 0, "27": 9, "274": 9, "28": 9, "2962": 0, "3": [1, 5, 7], "30": 11, "315": 7, "32995": 11, "33": [2, 8], "35": 7, "36995": 7, "382": 1, "38207": 7, "39": 9, "4": [2, 5, 7, 8, 11], "40": 11, "4000": 8, "41": 9, "416": 7, "422": 7, "433": 7, "45497": 7, "45504": 7, "45529": 7, "45545": 7, "45557": 7, "458d": 9, "471": 7, "4710": 9, "47485": 7, "49": 9, "49821": 7, "4de1": 9, "4ebc": 9, "5": [1, 2, 5, 7, 8], "50": [6, 11], "506": 7, "51247": 7, "517fdc524207": 9, "52": 9, "56": 9, "595": 1, "6": [1, 2, 5, 7, 8], "60": 11, "6353d6": 8, "64": 9, "7": 7, "70": [7, 11], "71619": 7, "76": 1, "79": 9, "8": [1, 7], "80": 11, "81853": 7, "82488e": 11, "82eeaa": 8, "83eb": 9, "87": 7, "88": 7, "89": 7, "8_13": 0, "90": 11, "90a5": 9, "92": 7, "92130": 7, "93": 7, "95": [1, 7], "97": 7, "970d": 9, "97797": 7, "977e4b4bbc46": 9, "978": 0, "9c52": 9, "9d": 8, "A": [0, 2, 7, 9], "For": [2, 5, 8, 10], "If": [0, 2, 8, 9], "In": 8, "It": [0, 2, 4, 5, 6, 7, 8, 9, 11], "NO": [2, 7], "No": [2, 11], "Not": 2, "Of": 0, "One": 8, "The": [0, 1, 2, 3, 4, 6, 7, 8, 9], "Then": [8, 10], "To": [5, 6, 7, 8, 9], "_opt": 2, "_out": 11, "aa1f": 9, "aaatt": 7, "aattg": 7, "about": [4, 10], "absolut": 8, "accept": 2, "access": [1, 10], "accordingli": [2, 8], "act": 2, "action": 3, "actrun_newdata_nanopore_uresnet20v2_model": 8, "ad": [2, 6, 7, 8, 9, 10], "add": [2, 8, 10], "addit": 9, "affect": 8, "after": 8, "algorithm": 7, "align": [0, 2, 7, 8, 9], "all": 6, "allow": 2, "alreadi": [2, 8], "also": [2, 8], "alwai": 11, "amazon": 5, "among": [2, 5], "amount": 2, "an": [2, 5, 6, 7, 8, 9, 10], "analysi": [0, 2, 4, 7, 8], "ani": [8, 11], "anna": [0, 8], "anno": [7, 9], "anoth": [7, 8], "appl": [5, 8], "ar": [2, 3, 5, 6, 7, 8, 9], "assembl": 8, "assembli": 8, "assign": [8, 9], "attga": 7, "authent": 10, "automat": [2, 5, 8], "avail": 8, "aw": [2, 5], "awsbatch": [2, 5], "ax": 8, "b5": 8, "b8d053": 8, "back": 10, "background": [6, 7, 8, 9], "bam": 8, "bambu": [2, 8], "barcod": [2, 11], "barcode01": 8, "barcode02": 8, "barcode_kit": 11, "barcodeid": 8, "base": [7, 8, 10], "basecal": [0, 2, 5, 9, 11], "basecallnew": 8, "basenam": 8, "bash": 5, "bash_profil": 10, "bashrc": 10, "batch": [2, 8], "bbb1": 9, "bc_1": 8, "bc_102": 8, "bc_104": 8, "bc_2": 8, "bc_3": 8, "becaus": 11, "bed": 2, "been": [7, 8], "befor": [5, 6, 7, 8, 9], "begin": 8, "being": [2, 5], "below": 7, "benchmark": 4, "beta": 2, "between": 0, "bg": [5, 6, 7, 8, 9, 10], "bin": 2, "biocor": 5, "biocorecrg": 5, "bioinformat": 0, "biol": 0, "bionextflow": 2, "both": [6, 7, 8, 9], "broken": 2, "bwa": 8, "c": [7, 8], "ca68": 9, "cach": 8, "call": [2, 8, 11], "caller": 11, "can": [0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11], "cannot": [8, 11], "card": 1, "case": 8, "cd": [5, 7, 8], "cdna": 2, "cdnaseq": [0, 4], "cf8c8c04cd3b": 9, "cfg": 8, "chang": [6, 7, 8, 9], "changelog": 4, "check": [3, 8, 11], "checkref": 8, "chemic": [0, 4], "chemistri": [2, 9], "chr": 7, "ci": 5, "cite": 0, "clone": 5, "cloud": [2, 5], "cluster": [2, 5, 8], "code": 7, "collect": 0, "column": 8, "com": [2, 5], "combin": 9, "come": 2, "command": [2, 6, 7, 8, 9, 11], "comparison": [6, 7], "compat": 5, "compil": 8, "complet": [2, 11], "compore_flow": 7, "compos": [0, 4], "comprehens": 10, "compress": [2, 5], "conf": 5, "config": [2, 6, 7, 8, 9], "configur": 5, "consensu": [0, 4, 6], "consid": 5, "contain": [5, 6, 7, 8, 9, 11], "content": 4, "contig": 7, "continu": [4, 5], "control": 8, "convent": 8, "convers": 2, "copi": 8, "core": 0, "correl": 9, "correspond": 8, "count": [0, 2, 8], "cov": 7, "coverag": 7, "coverage_ivt": 7, "coverage_sampl": 7, "cozzuto": 0, "cpu": [1, 10], "cram": [2, 8], "cram_fil": 8, "creat": [7, 8, 9], "crg": [0, 1, 2, 5, 8], "cuda11": 2, "curl": 5, "current": [5, 7], "custom": [2, 5], "dash": 8, "data": [0, 1, 4, 11], "dataset": [0, 2], "db70fb2cd130": 9, "decid": [6, 7, 8, 9], "dedic": 8, "deeplexicon": [2, 8], "deeplexicon_model": 8, "default": [5, 7], "del": 7, "delgado": 0, "delimit": 7, "demultiplex": [0, 2, 8], "depth": 5, "detail": [7, 8], "detect": [0, 4, 7, 8], "develop": 10, "difer": 6, "differ": [2, 5, 6, 7, 8, 9], "direct": [0, 2, 4], "directli": [0, 4], "directori": [6, 7, 8, 9, 11], "discov": 2, "discoveri": [2, 8], "disk": [2, 10], "distribut": 10, "dna": 2, "dnaseq": [0, 4], "do": [2, 8], "docker": [5, 6, 7, 8, 9, 10], "doi": 0, "don": 8, "dorado": [2, 8], "dorado_model": 8, "doubl": 11, "down": [2, 8], "download": [5, 8], "downsampl": 2, "downstream": [7, 8], "drna": 2, "drna_tool_m6a_splice_opt": 8, "drna_tool_splice_m6a_opt": 2, "dsl2": [0, 2, 4], "dure": 5, "dynam": 0, "e": 9, "e5": 8, "e5c990": 8, "each": [1, 2, 6, 7, 8, 10], "edit": 8, "either": [2, 5, 6, 7, 8, 9, 10, 11], "em": 0, "email": [6, 7, 9], "embed": 10, "emul": [5, 8], "ena": 1, "enabl": 10, "engin": 5, "environ": [5, 8, 10], "environment": 10, "epinano": [2, 7, 11], "epinano_flow": 7, "epinano_plot": 7, "epitranscriptom": 0, "err": 8, "err5296640": 1, "err5303454": 1, "error": [2, 8, 11], "estim": [0, 4, 9], "etc": [0, 4, 5, 8], "eu": 5, "eva": 0, "eventalign": 7, "eventu": 11, "exampl": [2, 6, 7, 8, 9, 10, 11], "execut": [1, 2, 5, 8, 10], "executor": 8, "explain": 8, "explan": 7, "export": 10, "extra": [2, 8], "extract": 2, "extrapar": 8, "extraparam": 6, "f": 8, "f5": [5, 8], "fa": [6, 7, 8, 9], "fast5": [2, 5, 7, 8, 9], "fast5_fil": 8, "faster": 2, "fastq": [2, 7, 8, 9, 11], "fastq_fil": 8, "fastqc": 11, "fb": 8, "fe6b": 9, "featur": [7, 8], "feed": [6, 7, 8, 9], "file": [2, 5, 6, 7, 8, 9, 10, 11], "fill": [6, 7, 9], "filter": [2, 8, 11], "final": [8, 10], "final_summary_": 2, "fine": 2, "finish": [10, 11], "first": 8, "flo": 11, "flow": 7, "flowcel": [2, 11], "folder": [1, 5, 7, 8, 9], "follow": [3, 6, 7, 8, 9, 10], "format": [2, 8], "formerli": 2, "four": [0, 4, 6, 7], "frequenc": 7, "from": [0, 2, 4, 5, 6, 8, 9], "front": 0, "function": 10, "furthermor": 8, "gaaga": 7, "gb": 1, "geforc": 1, "gene": [8, 9], "gene_a": 7, "gene_a_3": 7, "gene_a_4": 7, "gene_a_5": 7, "gene_a_6": 7, "gene_a_7": 7, "gene_a_8": 7, "gener": [0, 2, 4, 7, 8, 9, 10], "genet": 0, "genom": 8, "get": [2, 4], "getvers": 8, "git": 5, "github": [2, 3, 5, 10], "given": 8, "global": 2, "go": [8, 10], "good": [10, 11], "googl": 10, "gpu": [1, 2, 5], "graphmap": 8, "graphmap2": 8, "grid": 5, "group": 0, "guppi": [2, 8], "guppy65_basecal": 8, "guppy_vers": 8, "gz": [7, 8, 9], "gzip": 7, "h5": 8, "ha": [7, 8, 10], "had": 8, "handl": [0, 4], "have": [2, 5, 8, 10], "here": [6, 7, 8, 9, 10], "hermoso": 0, "hour": 1, "hpc": [1, 5, 8], "htseq": [2, 8], "http": [2, 5, 10], "huanl": 0, "i": [0, 2, 4, 5, 7, 8, 9, 10, 11], "id": [8, 9], "idea": 11, "improv": 2, "includ": 7, "independ": 2, "indic": [2, 8, 11], "individu": 7, "info": 2, "inform": [8, 10], "infrastructur": 5, "init": 11, "input": [0, 1, 11], "input_path": [6, 7, 9], "ins": 7, "insid": [2, 5], "inspir": 0, "instal": [2, 8], "instanc": 8, "instead": 2, "integr": [4, 5], "interest": 8, "intermedi": 8, "internet": 10, "io": 5, "isoqu": 2, "issu": 2, "its": [7, 10], "j": 0, "java": 5, "job": 1, "joint": 0, "julia": 0, "just": [5, 8, 10], "k14": 8, "keep_barcod": 2, "kept": [2, 8], "kind": 8, "kit": [2, 11], "known": 2, "ko": 7, "ko_1": 7, "ko_2": 7, "l": 0, "lab": 10, "laptop": 5, "later": [5, 7], "launch": [2, 6, 7, 8, 9, 10], "length": 9, "leszek": 0, "level": [7, 9], "like": [6, 7, 8, 9], "limit": [2, 8], "line": [2, 6, 7, 8, 9, 10], "link": 2, "linux": 5, "list": 8, "liu": 0, "local": [2, 5, 8, 10], "log": [5, 6, 7, 8, 9, 10], "look": 10, "low": [5, 11], "lsk114": 11, "luca": 0, "m": [8, 11], "m1": [5, 8], "m1mac": [5, 8], "m2": 5, "m3": 5, "m6a": 2, "make": 2, "mantain": 10, "map": [2, 8], "march": 0, "maria": 0, "master_of_por": 5, "masterofpor": [0, 2], "maximum": 1, "mb": 1, "medaka": 2, "median": 7, "memori": 10, "mer": 7, "merg": 2, "metallica": 0, "method": 0, "mi": 7, "min": 1, "min114": 11, "minimap2": [2, 8], "minion": 1, "mirror": 2, "mod": 8, "mode": [2, 9], "model": [2, 5, 7], "modelnam": 8, "modif": [0, 4], "modifi": 8, "modul": [2, 4, 7], "mol": 0, "mop": [1, 10], "mop2": 8, "mop3": 8, "mop3_pub": 5, "mop_consensu": [0, 1, 2, 4], "mop_mod": [0, 1, 2, 3, 4, 6], "mop_preprocess": [0, 1, 2, 3, 4, 5, 7, 9, 10], "mop_tail": [0, 1, 2, 3, 4], "more": [0, 7, 8], "multi": 8, "multifast5": 8, "multipl": 2, "multiqc": 8, "multithread": 2, "must": [8, 11], "myfil": 8, "n": 0, "n3ps_r10": [2, 9], "n3ps_r9": [2, 9], "na": 7, "name": [0, 8, 9], "nano3p": [2, 9], "nanocompor": 7, "nanoconsensu": 6, "nanocount": 8, "nanofilt": [8, 11], "nanomod": 2, "nanopolish": [7, 9], "nanopor": [0, 2, 4], "nanoporetech": 2, "nanopreprocess": 2, "nanopreprocesssimpl": 2, "nanoq": [8, 11], "nanoq_filt": 8, "nanotail": 2, "nbd114": 11, "need": [2, 5, 8], "netxtlow": 8, "new": [2, 8], "next": 8, "nextflow": [0, 2, 4, 5, 6, 7, 8, 9, 10], "nf": [5, 6, 7, 8, 9, 10], "nice": 10, "nm": 1, "novel": 8, "novoa": 0, "now": [2, 10], "number": 8, "o": 5, "obtain": 8, "off": 2, "old": 2, "onc": [7, 8, 10], "one": [2, 5, 6, 7, 8, 9], "ones": 2, "onli": [5, 8], "open": 11, "option": [2, 8], "origin": 2, "other": [2, 7, 8, 11], "otherwis": 8, "our": [0, 5, 7], "out": 11, "outfold": [7, 9], "output": [0, 1, 2, 4, 6, 7, 8, 9, 11], "output_mod": [6, 7], "outputpoli": 9, "oxford": [0, 2], "oxfordnanoport": 2, "p": [0, 7], "padsiz": 6, "pamp": 8, "paper": [0, 2], "parallel": [1, 2, 6], "param": [2, 5, 6, 7, 8, 9], "paramet": [2, 10], "pars_tool": [2, 7, 8, 9], "path": [2, 5, 6, 7, 8, 9], "peopl": 10, "per": [2, 7, 8, 11], "perform": [2, 7, 8], "pipelin": [0, 2, 3, 4, 5, 10], "place": [2, 5], "pleas": [0, 5, 6, 7, 8, 9], "plot": [2, 7, 9], "po": 7, "pod5": [2, 8], "poli": 9, "polya": [0, 4, 9], "polya_fin": 9, "ponomarenko": 0, "posit": 7, "posix": 5, "possibl": 2, "power": 2, "pre": [2, 8], "predict": [0, 4, 6, 7, 9], "prefer": 5, "preprocess": [0, 4], "present": 2, "prevent": 2, "previous": 8, "proce": 8, "process": [0, 2, 8, 10], "processor": [5, 8], "produc": 8, "profil": [2, 8, 10], "program": 9, "project": 0, "projectdir": [6, 7, 9], "protocol": 9, "provid": 9, "pryszcz": 0, "pu": 1, "public": 5, "publish": [1, 2], "pulido": 0, "puppet": 0, "q_mean": 7, "q_median": 7, "q_std": 7, "qc": 8, "qc_file": 8, "qualiti": [7, 8, 11], "quantifi": 2, "r10": [2, 9], "r9": [2, 9], "raw": [7, 8], "re": 8, "read": [0, 2, 4, 7, 8, 9, 11], "read_nam": 7, "readuck": [2, 8], "recommend": 10, "recurs": 5, "reduc": 2, "ref": 7, "ref_posit": 7, "refer": [6, 7, 8, 9], "reference_km": 7, "refin": 8, "remov": 11, "rep2": 8, "replac": 5, "repo": 5, "report": [4, 7, 8], "repositori": [2, 5, 7], "repres": [6, 7, 8, 9], "requir": [2, 5], "research": 0, "resnet20": 8, "resourc": [4, 5], "respect": [7, 8, 9], "rest": 8, "restrict": 8, "result": 2, "resum": [2, 8], "retriev": 2, "rewritten": 2, "right": 5, "rm": 11, "rna": [0, 2, 5, 7], "rna002_70bps_hac": 8, "rna_r9": 8, "rnaseq": [0, 4, 8], "row": 11, "rtx": 1, "run": [1, 2, 5, 10, 11], "sampl": [1, 7, 8, 11], "sample_processed_perpos_median": 7, "samplenam": 8, "savespac": 2, "schedul": 8, "section": 8, "see": [7, 8, 10], "select": [5, 8], "seq": 9, "seqera": 10, "seqfilt": 8, "sequenc": [0, 2, 8], "set": [2, 8], "sever": [7, 8, 9], "sge": [2, 5, 8], "sh": [2, 5], "should": [2, 6, 7, 8, 9, 10], "show": 9, "sinc": 10, "singl": 8, "singular": [5, 6, 7, 8, 9], "size": [0, 4, 9, 11], "slurm": [5, 8], "so": 8, "softwar": [0, 7], "solut": 11, "solv": 8, "some": [5, 8], "sometim": 11, "soon": 2, "space": 2, "special": 8, "specifi": [2, 6, 7, 8, 9], "splice": 8, "sqk": 11, "standard": [2, 9], "start": [2, 4, 8], "stat": 2, "step": [2, 7, 8], "store": [2, 5, 6, 7, 8, 9], "submit": 8, "submodul": 5, "subworkflow": 2, "successfulli": 11, "suggest": 10, "sum": 7, "sun": 5, "support": [2, 5, 8], "switch": [2, 5], "syntax": 2, "system": 5, "t": [0, 7, 8], "tab": 7, "tail": [0, 4, 9], "tailfind": 2, "tailfindr": [2, 9], "tailfindr_mod": [2, 9], "tailfinr": 9, "take": [6, 7, 8, 9], "tar": 5, "tejedor": 0, "temporari": [6, 7, 8, 9], "test": [1, 9], "test2": [6, 7, 8, 9], "text": 8, "tgaag": 7, "thank": 2, "thei": 8, "them": [5, 7, 8, 11], "thi": [0, 2, 6, 7, 8, 9, 10], "those": 2, "three": 9, "through": 5, "ti": 1, "time": [1, 2, 11], "togeth": [7, 9], "token": 10, "tombo": [2, 7], "tombo_flow": 7, "tombo_kmerscor": 7, "tombo_lsc": 7, "tombo_msc": 7, "tombo_sitescor": 7, "toni": 0, "too": 2, "tool": [0, 2, 6, 9, 11], "tool_opt": [2, 11], "tools_opt": [2, 6, 7, 9], "tower": 10, "tower_access_token": 10, "train1_newdata_nanopore_uresnet20v2_model": 8, "transcript": [2, 6, 7, 8, 9], "transcriptom": [7, 8], "trigger": 2, "troubleshoot": [4, 8], "tsv": [2, 6, 7, 8, 9], "ttgaa": 7, "tune": 2, "two": [1, 2, 7], "txt": [2, 6, 7, 8, 9], "uf": 8, "unsplic": 7, "up": [1, 5, 8, 11], "upgrad": 2, "us": [0, 1, 2, 3, 5, 6, 8, 9, 10, 11], "usag": 10, "user": [6, 7, 8, 9], "v3": 8, "valu": 7, "variabl": 10, "variant": 2, "vbz": [2, 5], "vbz_compress": 2, "version": [5, 8], "via": [2, 6, 7, 8, 9], "w": [6, 7, 8, 9], "wa": [1, 8], "want": [5, 8], "warm": 8, "warn": 2, "we": [1, 2, 5, 8, 10], "websit": 10, "well": [7, 8], "were": 8, "when": 2, "where": [1, 2], "which": [6, 7, 8, 9], "window": 5, "within": [5, 7, 8, 9], "without": 5, "won": 8, "work": [1, 6, 7, 8, 9], "workflow": [0, 2], "working_directori": [6, 7, 8, 9], "worklow": 6, "write": 8, "written": [0, 4], "wsl": 5, "wt": [7, 8], "wt_1": 7, "wt_1_vs_ko_1_nanocompore_result": 7, "wt_2": 7, "x": [2, 5, 8], "yaml": [5, 6, 7, 8, 9], "ydr133c": 9, "ye": [2, 7, 9], "yeast_rrna_ref": [7, 8, 9], "yet": 2, "yfl044c": 9, "ygl238w": 9, "ykr072c": 9, "you": [0, 2, 5, 6, 7, 8, 9, 10, 11], "your": [8, 10, 11], "yourdomain": 9, "yourlog": [7, 8], "yournam": 9}, "titles": ["About Master of Pores 3", "Benchmark", "CHANGELOG", "Continuous integration", "Welcome to the documentation of Master Of Pores 3", "Get Started", "MOP_CONSENSUS", "MOP_MOD", "MOP_PREPROCESS", "MOP_TAIL", "Resource reporting", "Troubleshooting"], "titleterms": {"0": 2, "1": 2, "2": 2, "3": [0, 2, 4], "Of": 4, "about": 0, "awar": [7, 8], "barcod": 8, "basecal": [7, 8], "benchmark": 1, "changelog": 2, "continu": 3, "data": 7, "dataset": 1, "demultiplex": 11, "document": 4, "encod": 7, "failur": 11, "from": 7, "get": 5, "guppi": [5, 11], "how": [6, 7, 8, 9], "html": 10, "inform": 7, "input": [6, 7, 8, 9], "instal": 5, "integr": 3, "librari": 8, "live": 10, "m6a": [7, 8], "master": [0, 4], "memori": 11, "model": 8, "modif": 7, "modphr": 7, "mop_consensu": 6, "mop_mod": [7, 11], "mop_preprocess": [8, 11], "mop_tail": 9, "paramet": [6, 7, 8, 9], "pipelin": [6, 7, 8, 9], "pore": [0, 4], "profil": 5, "refer": 0, "report": 10, "resourc": 10, "result": [6, 7, 8, 9], "run": [6, 7, 8, 9], "specif": 8, "start": 5, "test": 5, "tool": 8, "tool_opt": 8, "troubleshoot": 11, "us": 7, "version": 2, "welcom": 4}}) \ No newline at end of file