diff --git a/docs/images/pairgenomealgn-logo.png b/docs/images/pairgenomealgn-logo.png index 904ebab..6c12352 100644 Binary files a/docs/images/pairgenomealgn-logo.png and b/docs/images/pairgenomealgn-logo.png differ diff --git a/docs/images/pairgenomealgn-logo.svg b/docs/images/pairgenomealgn-logo.svg index 12ade50..d467777 100644 --- a/docs/images/pairgenomealgn-logo.svg +++ b/docs/images/pairgenomealgn-logo.svg @@ -2,49 +2,51 @@ - + + + + + + + + + + id="path8" /> + + + + + + + + + + id="g7" + transform="matrix(0.17674984,0.30899067,-0.95828269,0.16553372,206.43374,-49.649807)" + style="stroke-width:4.03224;stroke-dasharray:none"> + id="g8" + style="stroke-width:4.03224;stroke-dasharray:none"> + style="fill:none;stroke:#7eb2dd;stroke-width:4.03224;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;paint-order:markers fill stroke" + d="m 256.68383,89.400269 142.23004,0.580274" + id="path7" /> + + + + + + + + + + + + Indexseeds + seqtk cutN + assemblyscan + Target genome + TrainParameters + Alignquery(ies)on target + Query genome(s) + + + + fasta + + + + - - - - - + id="path10543" + d="m 598.73267,1905.0888 h -2.51304 v 12.1255 c 0,0.076 -0.0119,0.1518 -0.0221,0.2284 -0.004,0.4815 -0.15713,0.9544 -0.48679,1.3291 l -20.17826,23.0502 c -0.006,0.01 -0.0118,0.01 -0.0161,0.014 -0.12027,0.1343 -0.2605,0.246 -0.4087,0.3427 -0.0439,0.029 -0.0882,0.054 -0.13415,0.08 -0.12844,0.07 -0.26468,0.1282 -0.40491,0.1702 -0.038,0.011 -0.0722,0.026 -0.1102,0.036 -0.15238,0.036 -0.31066,0.059 -0.47103,0.059 h -49.59068 c -2.26452,0 -4.10417,-1.8417 -4.10417,-4.1044 v -33.3298 h -2.51247 c -3.23944,0 -5.86611,-2.6255 -5.86611,-5.8661 v -30.5048 c 0,-3.2383 2.62667,-5.8655 5.86611,-5.8655 h 2.51266 v -20.8815 c 0,-2.2624 1.83965,-4.1043 4.10417,-4.1043 h 67.71875 c 2.26242,0 4.10417,1.8417 4.10417,4.1043 v 20.8815 h 2.51304 c 3.23849,0 5.86573,2.6272 5.86573,5.8655 v 30.5039 c -1.9e-4,3.2404 -2.62743,5.8661 -5.86592,5.8661 z m -74.33596,33.33 h 47.5386 v -20.9983 c 0,-1.1338 0.91983,-2.0521 2.05208,-2.0521 h 18.12807 v -10.2809 h -67.71875 z m 67.71894,-95.336 h -67.71894 v 19.7705 h 67.71875 v -19.7705 z" + style="stroke-width:3.92686" /> + id="path10553" + d="m 524.39681,1938.4637 h 47.5386 v -20.9983 c 0,-1.1338 0.91983,-2.0521 2.05208,-2.0521 h 18.12807 v -10.2809 h -67.71875 z m 67.71894,-95.336 h -67.71894 v 19.7705 h 67.71875 v -19.7705 z" + style="fill:#ffffff;stroke-width:3.92686" /> + + + d="m 598.73267,1905.0888 h -2.51304 v 12.1255 c 0,0.076 -0.0119,0.1518 -0.0221,0.2284 -0.004,0.4815 -0.15713,0.9544 -0.48679,1.3291 l -20.17826,23.0502 c -0.006,0.01 -0.0118,0.01 -0.0161,0.014 -0.12027,0.1343 -0.2605,0.246 -0.4087,0.3427 -0.0439,0.029 -0.0882,0.054 -0.13415,0.08 -0.12844,0.07 -0.26468,0.1282 -0.40491,0.1702 -0.038,0.011 -0.0722,0.026 -0.1102,0.036 -0.15238,0.036 -0.31066,0.059 -0.47103,0.059 h -49.59068 c -2.26452,0 -4.10417,-1.8417 -4.10417,-4.1044 v -33.3298 h -2.51247 c -3.23944,0 -5.86611,-2.6255 -5.86611,-5.8661 v -30.5048 c 0,-3.2383 2.62667,-5.8655 5.86611,-5.8655 h 2.51266 v -20.8815 c 0,-2.2624 1.83965,-4.1043 4.10417,-4.1043 h 67.71875 c 2.26242,0 4.10417,1.8417 4.10417,4.1043 v 20.8815 h 2.51304 c 3.23849,0 5.86573,2.6272 5.86573,5.8655 v 30.5039 c -1.9e-4,3.2404 -2.62743,5.8661 -5.86592,5.8661 z m -74.33596,33.33 h 47.5386 v -20.9983 c 0,-1.1338 0.91983,-2.0521 2.05208,-2.0521 h 18.12807 v -10.2809 h -67.71875 z m 67.71894,-95.336 h -67.71894 v 19.7705 h 67.71875 v -19.7705 z" + id="path5862-6" + style="stroke-width:3.92686" /> + fasta - - - - - + style="fill:#ffffff;stroke-width:3.92686" + d="m 524.39681,1938.4637 h 47.5386 v -20.9983 c 0,-1.1338 0.91983,-2.0521 2.05208,-2.0521 h 18.12807 v -10.2809 h -67.71875 z m 67.71894,-95.336 h -67.71894 v 19.7705 h 67.71875 v -19.7705 z" + id="path6276-4-8" /> + + + + + png + + + + + png + + + + + + - - - + id="g6499" + transform="translate(-71.437497,78.58125)"> + - - - - - - - - - - - - - - - - - Index - seqtk cutN - assemblyscan - Target genome - Train alignmentparameters - Alignquery on target - Query genome(s) - One-to-onealignment(s) - One-to-onedotplot(s) - Many-to-onealignment(s) - Many-to-manyalignment(s) + + + + Postprocessing + Inputs QC + Dotplots + + Alignment + + One-to-manyalignment(s) + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.88056px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';opacity:0.99;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:none;stroke-width:1.32292;stroke-linecap:round;stroke-linejoin:round;stroke-opacity:0.717647" + x="33.11961" + y="138.97337" + id="text31-7-4-1-27">One-to-one + + + One-to-manydotplot(s) + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.88056px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';opacity:0.99;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:none;stroke-width:1.32292;stroke-linecap:round;stroke-linejoin:round;stroke-opacity:0.717647" + x="32.958553" + y="145.91557" + id="text31-7-4-1-5">Many-to-one + + + Many-to-onedotplot(s) + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.88056px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';opacity:0.99;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:none;stroke-width:1.32292;stroke-linecap:round;stroke-linejoin:round;stroke-opacity:0.717647" + x="85.39341" + y="129.49086" + id="text31-7-49-1">Outputs + + + Many-to-manydotplot(s) - + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.88056px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';opacity:0.99;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:none;stroke-width:1.32292;stroke-linecap:round;stroke-linejoin:round;stroke-opacity:0.717647" + x="51.526737" + y="129.49086" + id="text31-7-49-7">modules + + + + id="g4374-5-7-1" + transform="matrix(1.020815,0,0,1.020815,137.89782,342.66379)" + style="stroke-width:1.32402"> + v1.0 + + + + + - - - - - - - - - - + id="g4301-8" + style="stroke-width:0.976389"> + + + + + + + + + + - - + nf-nf- - core - - + x="277.43979" + class="st0 st1 st2">core/ + + + + One-to-many + style="opacity:0.99;fill:#000000;fill-opacity:0.294821;fill-rule:evenodd;stroke:#f697f4;stroke-width:1.546;stroke-linecap:round;stroke-linejoin:round;stroke-dasharray:none;stroke-opacity:0.564706;paint-order:markers fill stroke" + d="m 14.273359,152.1519 c 3.817768,0 7.63552,0 11.453282,0" + id="path99-3" /> + + + Target genome + + + Pairgenomealign pipeline + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.88056px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';opacity:0.99;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:none;stroke-width:1.32292;stroke-linecap:round;stroke-linejoin:round;stroke-opacity:0.717647" + x="33.11961" + y="167.89035" + id="text31-7-4-1">Query genome(s) + + - 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- + + + maf - - - - - maf + + + + + maf - + id="text91" + transform="scale(1,-1)"> maf + + - + id="g128"> + + + maf - + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:4.93889px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';opacity:0.99;fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:none;stroke-width:1.32292;stroke-linecap:round;stroke-linejoin:round;stroke-opacity:0.717647" + x="225.66367" + y="194.92166" + id="text31-7-3-1-3">Many-tomany + + + png + + - - - + + + + + maf + + + + + + + maf - - + id="tspan89" + style="font-size:27.538px;stroke-width:4.0583px"> maf + + + + + + Many-toone + png png + + + + + + maf + + + + + + + + + + + + + + + + + + + + maf + + + + + One-toone + + png png - Query genome(s) - Target genome - - - - - - pairgenome - align - - -