doc/workflow.drawio.svg

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                Output
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                Input
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                                Data Type
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                    Data Type
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                                <b style="font-size: 14px">
                                    Raw Reads
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                                    *_{,R}{1,2}{,_001}.{fq,fastq}{,.gz}
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                    Raw Reads...
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                                FASTQ (Reads)
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                    FASTQ (Reads)
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                S. Pneumo:     ≥ 60%
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                Other Genus:  ≤ 2%
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                Contigs:  ≤ 500
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                Length:   1.9 - 2.3 Mb
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                Depth:     ≥ 20x
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                                FASTA (Assemblies)
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                    FASTA (Assemblies)
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                                SAM
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                    SAM
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                Ref Coverage: ≥ 60%
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                Het-SNP site:  ≤ 220
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                                Results
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                    Results
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                                <b style="font-size: 14px">
                                    Assembly
                                </b>
                                <br style="font-size: 14px"/>
                                SPAdes
                                <br/>
                                <font style="font-size: 12px;">
                                    (Default: Shovill)
                                </font>
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                    Asse...
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                                <b style="font-size: 14px">
                                    Mapping
                                </b>
                                <br style="font-size: 14px"/>
                                BWA MEM
                            </div>
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                    </div>
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                <text x="595" y="442" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Mapp...
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                                <div style="font-size: 14px">
                                    <b style="font-size: 14px">
                                        Taxonomy &amp; Taxonomy QC
                                    </b>
                                </div>
                                <div style="font-size: 14px">
                                    Kraken 2
                                </div>
                            </div>
                        </div>
                    </div>
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                <text x="595" y="337" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Taxo...
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                                <b style="border-color: var(--border-color);">
                                    Assembly QC
                                </b>
                                <br style="font-size: 14px;"/>
                                QUAST
                            </div>
                        </div>
                    </div>
                </foreignObject>
                <text x="715" y="537" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Asse...
                </text>
            </switch>
        </g>
        <ellipse cx="715" cy="460" rx="15" ry="15" fill="#d5e8d4" stroke="#82b366" stroke-width="2" pointer-events="all"/>
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                                <b style="border-color: var(--border-color);">
                                    Mapping QC
                                </b>
                                <b style="font-size: 14px">
                                    <br style="font-size: 14px"/>
                                </b>
                                SAMtools, BCFtools,
                                <br/>
                                custom script
                            </div>
                        </div>
                    </div>
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                <text x="715" y="442" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Mapp...
                </text>
            </switch>
        </g>
        <path d="M 370 385 L 390 385 Q 400 385 400 375 L 400 290 Q 400 280 410 280 L 930 280 Q 940 280 940 290 L 940 432.92 Q 940 442.92 950 442.92 L 989.91 442.92" fill="none" stroke="#9673a6" stroke-width="5" stroke-miterlimit="10" pointer-events="stroke"/>
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                                <b style="font-size: 14px;">
                                    Preprocess
                                </b>
                                <br style="font-size: 14px;"/>
                                fastp
                            </div>
                        </div>
                    </div>
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                <text x="305" y="496" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Prep...
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            </switch>
        </g>
        <path d="M 1225 485 L 1290 485 Q 1300 485 1300 475 L 1300 467.5 Q 1300 460 1310 460 L 1460 460" fill="none" stroke="#9673a6" stroke-width="5" stroke-miterlimit="10" pointer-events="stroke"/>
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                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe flex-end; justify-content: unsafe center; width: 1px; height: 1px; padding-top: 467px; margin-left: 1210px;">
                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
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                                <b style="font-size: 14px">
                                    PBP AMR
                                </b>
                                <br style="font-size: 14px"/>
                                CDC PBP AMR Predictor
                            </div>
                        </div>
                    </div>
                </foreignObject>
                <text x="1210" y="467" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    PBP...
                </text>
            </switch>
        </g>
        <path d="M 1225 404 L 1290 404 Q 1300 404 1300 414 L 1300 450 Q 1300 460 1310 460 L 1460 460" fill="none" stroke="#9673a6" stroke-width="5" stroke-miterlimit="10" pointer-events="stroke"/>
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                                <b style="font-size: 14px">
                                    MLST
                                </b>
                                <br style="font-size: 14px"/>
                                mlst
                            </div>
                        </div>
                    </div>
                </foreignObject>
                <text x="1210" y="386" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    MLST...
                </text>
            </switch>
        </g>
        <path d="M 1005 455 L 1050 455 Q 1060 455 1060 445 L 1060 250 Q 1060 240 1070 240 L 1290 240 Q 1300 240 1300 250 L 1300 450 Q 1300 460 1310 460 L 1460 460" fill="none" stroke="#9673a6" stroke-width="5" stroke-miterlimit="10" pointer-events="stroke"/>
        <path d="M 1005 455 L 1050 455 Q 1060 455 1060 465 L 1060 600" fill="none" stroke="#9673a6" stroke-width="5" stroke-miterlimit="10" pointer-events="stroke"/>
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            <switch>
                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe flex-end; justify-content: unsafe center; width: 1px; height: 1px; padding-top: 432px; margin-left: 1005px;">
                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
                            <div style="display: inline-block; font-size: 14px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: nowrap;">
                                <b style="font-size: 14px">
                                    Overall QC
                                </b>
                            </div>
                        </div>
                    </div>
                </foreignObject>
                <text x="1005" y="432" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Over...
                </text>
            </switch>
        </g>
        <path d="M 1225 324 L 1290 324 Q 1300 324 1300 334 L 1300 450 Q 1300 460 1310 460 L 1460 460" fill="none" stroke="#9673a6" stroke-width="5" stroke-miterlimit="10" pointer-events="stroke"/>
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        <g transform="translate(-0.5 -0.5)">
            <switch>
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                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe flex-end; justify-content: unsafe center; width: 1px; height: 1px; padding-top: 306px; margin-left: 1210px;">
                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
                            <div style="display: inline-block; font-size: 14px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: nowrap;">
                                <b style="font-size: 14px">
                                    Lineage
                                </b>
                                <br style="font-size: 14px"/>
                                PopPUNK
                            </div>
                        </div>
                    </div>
                </foreignObject>
                <text x="1210" y="306" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Line...
                </text>
            </switch>
        </g>
        <path d="M 1225 645 L 1290 645 Q 1300 645 1300 635 L 1300 470 Q 1300 460 1310 460 L 1460 460" fill="none" stroke="#9673a6" stroke-width="5" stroke-miterlimit="10" pointer-events="stroke"/>
        <ellipse cx="1210" cy="645" rx="15" ry="15" fill="#d5e8d4" stroke="#82b366" stroke-width="2" pointer-events="all"/>
        <g transform="translate(-0.5 -0.5)">
            <switch>
                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe flex-end; justify-content: unsafe center; width: 1px; height: 1px; padding-top: 627px; margin-left: 1210px;">
                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
                            <div style="display: inline-block; font-size: 14px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: nowrap;">
                                <b style="font-size: 14px;">
                                    Serotype
                                </b>
                                <br style="font-size: 14px;"/>
                                SeroBA
                            </div>
                        </div>
                    </div>
                </foreignObject>
                <text x="1210" y="627" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Sero...
                </text>
            </switch>
        </g>
        <path d="M 1225 565 L 1290 565 Q 1300 565 1300 555 L 1300 470 Q 1300 460 1310 460 L 1460 460" fill="none" stroke="#9673a6" stroke-width="5" stroke-miterlimit="10" pointer-events="stroke"/>
        <path d="M 1535 322 C 1537.76 322 1540 324.24 1540 327 L 1540 364 Q 1520 353.2 1500 364 Q 1480 374.8 1460 364 L 1460 328 L 1460 327 C 1460 324.24 1462.24 322 1465 322 Z" fill="rgb(255, 255, 255)" stroke="rgb(0, 0, 0)" stroke-width="2" stroke-miterlimit="10" pointer-events="all"/>
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                                <b style="font-size: 14px">
                                    Information
                                </b>
                                <br style="font-size: 14px"/>
                                info.txt
                            </div>
                        </div>
                    </div>
                </foreignObject>
                <text x="1500" y="316" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Informatio...
                </text>
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        <g fill="rgb(0, 0, 0)" font-family="Helvetica" font-style="italic" font-size="12px">
            <text x="311.5" y="412.5">
                Bases: ≥ 38 Mb
            </text>
        </g>
        <path d="M 1069.96 609.84 L 1130 609.84 Q 1140 609.84 1140 599.84 L 1140 575 Q 1140 565 1150 565 L 1195 565" fill="none" stroke="#b85450" stroke-width="5" stroke-miterlimit="10" pointer-events="stroke"/>
        <path d="M 1469.09 563.98 C 1469.09 561.78 1471.13 560 1473.64 560 L 1535.45 560 C 1537.96 560 1540 561.78 1540 563.98 L 1540 595.83 C 1528.67 591.63 1515.88 591.63 1504.55 595.83 C 1493.21 600.04 1480.42 600.04 1469.09 595.83 Z" fill="rgb(255, 255, 255)" stroke="rgb(0, 0, 0)" stroke-width="2" stroke-miterlimit="10" pointer-events="all"/>
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        <path d="M 1460 571.94 C 1460 569.75 1462.04 567.96 1464.55 567.96 L 1526.36 567.96 C 1528.87 567.96 1530.91 569.75 1530.91 571.94 L 1530.91 603.8 C 1519.58 599.59 1506.79 599.59 1495.45 603.8 C 1484.12 608 1471.33 608 1460 603.8 Z" fill="rgb(255, 255, 255)" stroke="rgb(0, 0, 0)" stroke-width="2" stroke-miterlimit="10" pointer-events="all"/>
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                                <b style="font-size: 14px">
                                    Assemblies
                                </b>
                                <br style="font-size: 14px"/>
                                assemblies/*.contigs.fasta
                            </div>
                        </div>
                    </div>
                </foreignObject>
                <text x="1500" y="554" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Assemblies...
                </text>
            </switch>
        </g>
        <path d="M 1535 436 C 1537.76 436 1540 438.24 1540 441 L 1540 478 Q 1520 467.2 1500 478 Q 1480 488.8 1460 478 L 1460 442 L 1460 441 C 1460 438.24 1462.24 436 1465 436 Z" fill="rgb(255, 255, 255)" stroke="rgb(0, 0, 0)" stroke-width="2" stroke-miterlimit="10" pointer-events="all"/>
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                                <b style="font-size: 14px">
                                    Results
                                </b>
                                <br style="font-size: 14px"/>
                                results.csv
                            </div>
                        </div>
                    </div>
                </foreignObject>
                <text x="1500" y="430" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="14px" text-anchor="middle">
                    Results...
                </text>
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                                    Read QC
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                QC values shown in the diagram are the default values
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                Go / No-go
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                                <b>
                                    Other AMR / Virulence
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                                <br/>
                                ARIBA, custom script
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                Go / No-go
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