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comparison test-data/test2_report.html @ 9:45924fa8d8c5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
author iuc
date Mon, 08 Nov 2021 09:03:00 +0000
parents 81df4950d65b
children 875d0f36d66f
comparison
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8:ebb0dcdb621a 9:45924fa8d8c5
2649 </script> 2649 </script>
2650 2650
2651 <script type="text/javascript"> 2651 <script type="text/javascript">
2652 2652
2653 var gns = { 2653 var gns = {
2654 genes: { 2654 features: {
2655 isInitialized: false, 2655 isInitialized: false,
2656 2656
2657 maxY: 0, 2657 maxY: 0,
2658 maxYTick: 0, 2658 maxYTick: 0,
2659 series: null, 2659 series: null,
2671 showWithData: null, 2671 showWithData: null,
2672 2672
2673 yAxisLabeled: false 2673 yAxisLabeled: false
2674 }, 2674 },
2675 2675
2676 draw: function (name, title, colors, filenames, data, refGenesNumber, tickX, 2676 draw: function (name, title, colors, filenames, data, refFeaturesNumber, tickX,
2677 placeholder, legendPlaceholder, glossary, order, scalePlaceholder) { 2677 placeholder, legendPlaceholder, glossary, order, scalePlaceholder) {
2678 // div.html( 2678 // div.html(
2679 // "<span class='plot-header'>" + kind[0].toUpperCase() + kind.slice(1) + "s covered</span>" + 2679 // "<span class='plot-header'>" + kind[0].toUpperCase() + kind.slice(1) + "s covered</span>" +
2680 // "<div class='plot-placeholder' id='" + kind + "s-plot-placeholder'></div>" 2680 // "<div class='plot-placeholder' id='" + kind + "s-plot-placeholder'></div>"
2681 // ); 2681 // );
2693 info.series = new Array(plotsN); 2693 info.series = new Array(plotsN);
2694 2694
2695 info.maxY = 0; 2695 info.maxY = 0;
2696 info.maxX = 0; 2696 info.maxX = 0;
2697 2697
2698 if (refGenesNumber) { 2698 if (refFeaturesNumber) {
2699 info.maxY = refGenesNumber; 2699 info.maxY = refFeaturesNumber;
2700 } 2700 }
2701 2701
2702 for (var fi = 0; fi < plotsN; fi++) { 2702 for (var fi = 0; fi < plotsN; fi++) {
2703 var index = $.inArray(cur_filenames[order[fi]], filenames); 2703 var index = $.inArray(cur_filenames[order[fi]], filenames);
2704 var filename = filenames[index]; 2704 var filename = filenames[index];
2752 // fill: 1, 2752 // fill: 1,
2753 // fillColor: false, 2753 // fillColor: false,
2754 // } 2754 // }
2755 // } 2755 // }
2756 2756
2757 if (refGenesNumber) { 2757 if (refFeaturesNumber) {
2758 info.series.push({ 2758 info.series.push({
2759 data: [[0, refGenesNumber], [info.maxX, refGenesNumber]], 2759 data: [[0, refFeaturesNumber], [info.maxX, refFeaturesNumber]],
2760 label: 'reference,&nbsp;' + toPrettyString(refGenesNumber, 'genes'), 2760 label: 'reference,&nbsp;' + toPrettyString(refFeaturesNumber, 'features'),
2761 isReference: true, 2761 isReference: true,
2762 dashes: { 2762 dashes: {
2763 show: true, 2763 show: true,
2764 lineWidth: 1 2764 lineWidth: 1
2765 }, 2765 },
2822 }; 2822 };
2823 2823
2824 info.isInitialized = true; 2824 info.isInitialized = true;
2825 } 2825 }
2826 2826
2827 addLegendClickEvents(info, filenames.length, showPlotWithInfo, refGenesNumber); 2827 addLegendClickEvents(info, filenames.length, showPlotWithInfo, refFeaturesNumber);
2828 2828
2829 showPlotWithInfo(info); 2829 showPlotWithInfo(info);
2830 2830
2831 $('#contigs_are_ordered').show(); 2831 $('#contigs_are_ordered').show();
2832 } 2832 }
4212 referenceValues[metricName] = value; 4212 referenceValues[metricName] = value;
4213 } 4213 }
4214 var refLen = referenceValues['Reference length']; 4214 var refLen = referenceValues['Reference length'];
4215 var refFragments = referenceValues['Reference fragments']; 4215 var refFragments = referenceValues['Reference fragments'];
4216 var refGC = referenceValues['Reference GC (%)']; 4216 var refGC = referenceValues['Reference GC (%)'];
4217 var refGenes = referenceValues['Reference genes']; 4217 var refFeatures = referenceValues['Reference genomic features'];
4218 var refOperons = referenceValues['Reference operons']; 4218 var refOperons = referenceValues['Reference operons'];
4219 var refChr = referenceValues['Reference chromosomes']; 4219 var refChr = referenceValues['Reference chromosomes'];
4220 var totalReads = referenceValues['# total reads']; 4220 var totalReads = referenceValues['# total reads'];
4221 var refMappedReads = referenceValues['Reference mapped (%)']; 4221 var refMappedReads = referenceValues['Reference mapped (%)'];
4222 var refPairedReads = referenceValues['Reference properly paired (%)']; 4222 var refPairedReads = referenceValues['Reference properly paired (%)'];
4231 if (refFragments > 1) 4231 if (refFragments > 1)
4232 $('#reference_fragments').find('.plural_ending').show(); 4232 $('#reference_fragments').find('.plural_ending').show();
4233 } 4233 }
4234 if (refGC) 4234 if (refGC)
4235 $('#reference_gc').show().find('.val').html(toPrettyString(refGC)); 4235 $('#reference_gc').show().find('.val').html(toPrettyString(refGC));
4236 if (refGenes) 4236 if (refFeatures)
4237 $('#reference_genes').show().find('.val').html(toPrettyString(refGenes)); 4237 $('#reference_features').show().find('.val').html(toPrettyString(refFeatures));
4238 if (refOperons) 4238 if (refOperons)
4239 $('#reference_operons').show().find('.val').html(toPrettyString(refOperons)); 4239 $('#reference_operons').show().find('.val').html(toPrettyString(refOperons));
4240 if (refChr) { 4240 if (refChr) {
4241 $('#reference_chr').show().find('.val').html(refChr); 4241 $('#reference_chr').show().find('.val').html(refChr);
4242 if (refChr > 1) 4242 if (refChr > 1)
4320 var coordNx = null; 4320 var coordNx = null;
4321 var contigsLensNx = null; 4321 var contigsLensNx = null;
4322 var alignedContigsLens = null; 4322 var alignedContigsLens = null;
4323 var refLengths = null; 4323 var refLengths = null;
4324 var contigs = null; 4324 var contigs = null;
4325 var genesInContigs = null; 4325 var featuresInContigs = null;
4326 var operonsInContigs = null; 4326 var operonsInContigs = null;
4327 var gcInfos = null; 4327 var gcInfos = null;
4328 4328
4329 var glossary = JSON.parse($('#glossary-json').html()); 4329 var glossary = JSON.parse($('#glossary-json').html());
4330 4330
4425 null, 1 4425 null, 1
4426 ); 4426 );
4427 firstPlot = false; 4427 firstPlot = false;
4428 } 4428 }
4429 4429
4430 genesInContigs = readJson('genes-in-contigs'); 4430 featuresInContigs = readJson('features-in-contigs');
4431 operonsInContigs = readJson('operons-in-contigs'); 4431 operonsInContigs = readJson('operons-in-contigs');
4432 // if (genesInContigs || operonsInContigs) 4432 // if (genesInContigs || operonsInContigs)
4433 // contigs = readJson('contigs'); 4433 // contigs = readJson('contigs');
4434 4434
4435 if (genesInContigs) { 4435 if (featuresInContigs) {
4436 makePlot(firstPlot, assembliesNames, order, 'genes', 'Genes', gns.draw, { 4436 makePlot(firstPlot, assembliesNames, order, 'features', 'Genomic features', gns.draw, {
4437 filesFeatureInContigs: genesInContigs.genes_in_contigs, 4437 filesFeatureInContigs: featuresInContigs.features_in_contigs,
4438 kind: 'gene', 4438 kind: 'gene',
4439 filenames: genesInContigs.filenames 4439 filenames: featuresInContigs.filenames
4440 }, 4440 },
4441 genesInContigs.ref_genes_number, tickX 4441 featuresInContigs.ref_features_number, tickX
4442 ); 4442 );
4443 firstPlot = false; 4443 firstPlot = false;
4444 } 4444 }
4445 if (operonsInContigs) { 4445 if (operonsInContigs) {
4446 makePlot(firstPlot, assembliesNames, order, 'operons', 'Operons', gns.draw, { 4446 makePlot(firstPlot, assembliesNames, order, 'operons', 'Operons', gns.draw, {
4562 4562
4563 <span style="display: none;" id="reference_paired_reads">| 4563 <span style="display: none;" id="reference_paired_reads">|
4564 <span class='val'></span>% properly paired 4564 <span class='val'></span>% properly paired
4565 </span> 4565 </span>
4566 4566
4567 <span style="display: none;" id="reference_genes"><br> 4567 <span style="display: none;" id="reference_features"><br>
4568 <span class='val'></span> genes 4568 <span class='val'></span> genomic features
4569 </span> 4569 </span>
4570 4570
4571 <span style="display: none;" id="reference_operons">| 4571 <span style="display: none;" id="reference_operons">|
4572 <span class='val'></span> operons 4572 <span class='val'></span> operons
4573 </span> 4573 </span>
4637 <div style="clear: left"></div> 4637 <div style="clear: left"></div>
4638 <div style="clear: right"></div> 4638 <div style="clear: right"></div>
4639 4639
4640 <div class='json-code'> 4640 <div class='json-code'>
4641 <div id='total-report-json'> 4641 <div id='total-report-json'>
4642 {"date":"03 December 2018, Monday, 23:14:03","assembliesNames":["contigs2_fna","contigs1_fna"],"referenceName":"","order":[0,1],"report":[["Genome statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N's","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[1,3],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[1,3],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[1,3],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[6650,3980],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6650,6710],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6650,6710],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6650,6710],"isMain":true},{"metricName":"N50","quality":"More is better","values":[6650,3980],"isMain":false},{"metricName":"N75","quality":"More is better","values":[6650,1610],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[1,2],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["52.00","51.28"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500} 4642 {"date":"07 November 2021, Sunday, 18:59:15","assembliesNames":["contig1","contig2"],"referenceName":"dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74","order":[0,1],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["71.579","100.000"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.000","1.000"],"isMain":true},{"metricName":"# genomic features","quality":"More is better","values":["7 + 7 part","13 + 1 part"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[2030,6650],"isMain":true},{"metricName":"Total aligned length","quality":"More is better","values":[4760,6650],"isMain":true},{"metricName":"NG50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"NG75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA50","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"NGA50","quality":"More is better","values":[1610,6650],"isMain":true},{"metricName":"NGA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"LG50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"LG75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA50","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA75","quality":"Less is better","values":[null,1],"isMain":false},{"metricName":"LGA50","quality":"Less is better","values":[2,1],"isMain":true},{"metricName":"LGA75","quality":"Less is better","values":[null,1],"isMain":false}]],["Reads mapping",[]],["Misassemblies",[{"metricName":"# misassemblies","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # relocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # translocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # inversions","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# misassembled contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Misassembled contigs length","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":"# local misassemblies","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap ext. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap loc. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# unaligned mis. contigs","quality":"Less is better","values":[0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Fully unaligned length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[1,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[1950,0],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# indels","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N's","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[{"metricName":"K-mer-based compl. (%)","quality":"More is better","values":["68.09","100.00"],"isMain":true},{"metricName":"K-mer-based cor. length (%)","quality":"More is better","values":["100.00","100.00"],"isMain":false},{"metricName":"K-mer-based mis. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"K-mer-based undef. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"# k-mer-based misjoins","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # k-mer-based translocations","quality":"Equal","values":[0,0],"isMain":false},{"metricName":" # k-mer-based 100kbp relocations","quality":"Equal","values":[0,0],"isMain":false}]],["Predicted genes",[]],["Similarity statistics",[{"metricName":"# similar correct contigs","quality":"Equal","values":[0,0],"isMain":false},{"metricName":"# similar misassembled blocks","quality":"Equal","values":[0,0],"isMain":false}]],["Reference statistics",[{"metricName":"Reference length","quality":"Equal","values":[6650,6650],"isMain":false},{"metricName":"Reference fragments","quality":"Equal","values":[1,1],"isMain":false},{"metricName":"Reference GC (%)","quality":"Equal","values":["52.00","52.00"],"isMain":false},{"metricName":"Reference genomic features","quality":"Equal","values":[14,14],"isMain":false},{"metricName":"Reference operons","quality":"Equal","values":[0,0],"isMain":false}]]],"subreferences":[],"subreports":[],"minContig":500}
4643 </div> 4643 </div>
4644 <div id='qualities-json'> 4644 <div id='qualities-json'>
4645 {{ qualities }} 4645 {{ qualities }}
4646 </div> 4646 </div>
4647 <div id='main-metrics-json'> 4647 <div id='main-metrics-json'>
4648 {{ mainMetrics }} 4648 {{ mainMetrics }}
4649 </div> 4649 </div>
4650 4650
4651 <div id="contigs-lengths-json"> 4651 <div id="contigs-lengths-json">
4652 {"filenames":["contigs2_fna","contigs1_fna"],"lists_of_lengths":[[6650],[3980,1610,1120]]} 4652 {"filenames":["contig1","contig2"],"lists_of_lengths":[[3980,1610,1120],[6650]]}
4653 </div> 4653 </div>
4654 <div id='assemblies-lengths-json'> 4654 <div id='assemblies-lengths-json'>
4655 {{ assembliesLengths }} 4655 {"filenames":["contig1","contig2"],"assemblies_lengths":[6710,6650]}
4656 </div> 4656 </div>
4657 <div id='reference-length-json'> 4657 <div id='reference-length-json'>
4658 {{ referenceLength }} 4658 {"reflen":[6650]}
4659 </div> 4659 </div>
4660 <div id='tick-x-json'> 4660 <div id='tick-x-json'>
4661 {"tickX":1} 4661 {"tickX":1}
4662 </div> 4662 </div>
4663 <div id='coord-nx-json'> 4663 <div id='coord-nx-json'>
4664 {"coord_x":[[0.0,1e-10,100.0,100.0000000001],[0.0,1e-10,59.31445603576751,59.314456035867515,83.30849478390462,83.30849478400462,100.0,100.0000000001]],"coord_y":[[6650,6650,6650,0.0],[3980,3980,3980,1610,1610,1120,1120,0.0]],"filenames":["contigs2_fna","contigs1_fna"]} 4664 {"coord_x":[[0.0,1e-10,59.31445603576751,59.314456035867515,83.30849478390462,83.30849478400462,100.0,100.0000000001],[0.0,1e-10,100.0,100.0000000001]],"coord_y":[[3980,3980,3980,1610,1610,1120,1120,0.0],[6650,6650,6650,0.0]],"filenames":["contig1","contig2"]}
4665 </div> 4665 </div>
4666 <div id='coord-ngx-json'> 4666 <div id='coord-ngx-json'>
4667 {{ coordNGx }} 4667 {"coord_x":[[0.0,1e-10,59.849624060150376,59.84962406025038,84.06015037593986,84.06015037603986,100.90225563909775,100.90225563919775],[0.0,1e-10,100.0,100.0000000001]],"coord_y":[[3980,3980,3980,1610,1610,1120,1120,0.0],[6650,6650,6650,0.0]],"filenames":["contig1","contig2"]}
4668 </div> 4668 </div>
4669 <div id='coord-nax-json'> 4669 <div id='coord-nax-json'>
4670 {{ coordNAx }} 4670 {"coord_x":[[0.0,1e-10,30.253353204172875,30.253353204272873,54.24739195230998,54.247391952409984,70.93889716840536,70.93889716850536],[0.0,1e-10,100.0,100.0000000001]],"coord_y":[[2030,2030,2030,1610,1610,1120,1120,0.0],[6650,6650,6650,0.0]],"filenames":["contig1","contig2"]}
4671 </div> 4671 </div>
4672 <div id='coord-ngax-json'> 4672 <div id='coord-ngax-json'>
4673 {{ coordNGAx }} 4673 {"coord_x":[[0.0,1e-10,30.526315789473685,30.526315789573683,54.73684210526316,54.73684210536316,71.57894736842105,71.57894736852106],[0.0,1e-10,100.0,100.0000000001]],"coord_y":[[2030,2030,2030,1610,1610,1120,1120,0.0],[6650,6650,6650,0.0]],"filenames":["contig1","contig2"]}
4674 </div> 4674 </div>
4675 <div id='coord-misassemblies-json'> 4675 <div id='coord-misassemblies-json'>
4676 {{ coordmisassemblies }} 4676 {"coord_x":[[0,1],[0,1]],"coord_y":[[71.57894736842105,71.57894736842105],[100.0,100.0]],"filenames":["contig1","contig2"]}
4677 </div> 4677 </div>
4678 <div id='genes-in-contigs-json'> 4678 <div id='features-in-contigs-json'>
4679 {{ genesInContigs }} 4679 {"filenames":["contig1","contig2"],"features_in_contigs":{"contig1":[5,0,2],"contig2":[13]},"ref_features_number":14}
4680 </div> 4680 </div>
4681 <div id='operons-in-contigs-json'> 4681 <div id='operons-in-contigs-json'>
4682 {{ operonsInContigs }} 4682 {{ operonsInContigs }}
4683 </div> 4683 </div>
4684 <div id='summary-json'> 4684 <div id='summary-json'>
4699 </div> 4699 </div>
4700 <div id='krona-json'> 4700 <div id='krona-json'>
4701 {{ krona }} 4701 {{ krona }}
4702 </div> 4702 </div>
4703 <div id='gc-json'> 4703 <div id='gc-json'>
4704 {"filenames":["contigs2_fna","contigs1_fna"],"reference_index":null,"list_of_GC_distributions":[[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,3,2,1,0,0,5,3,4,4,7,3,5,2,4,7,0,10,1,1,2,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,3,1,0,1,2,1,5,5,5,2,5,4,4,7,1,6,2,5,1,0,1,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"list_of_GC_contigs_distributions":[[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null} 4704 {"filenames":["contig1","contig2"],"reference_index":2,"list_of_GC_distributions":[[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,3,1,0,1,2,1,5,5,5,2,5,4,4,7,1,6,2,5,1,0,1,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,3,2,1,0,0,5,3,4,4,7,3,5,2,4,7,0,10,1,1,2,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,3,2,1,0,0,5,3,4,4,7,3,5,2,4,7,0,10,1,1,2,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"list_of_GC_contigs_distributions":[[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null}
4705 </div> 4705 </div>
4706 <div id='icarus-json'> 4706 <div id='icarus-json'>
4707 {"links":["icarus_viewers/contig_size_viewer.html"],"links_names":["View in Icarus contig browser"]} 4707 {"links":["icarus_viewers/alignment_viewer.html"],"links_names":["View in Icarus contig browser"]}
4708 </div> 4708 </div>
4709 </div> 4709 </div>
4710 </div> 4710 </div>
4711 4711
4712 <div class='json-code'> 4712 <div class='json-code'>
4787 "# genomic features" : "<span>is the number of genomic features (genes, transcripts, CDS) in the assembly (complete and partial), based on a user-provided annotated list of gene positions in the reference genome. A feature counts as 'partially covered' if the assembly contains at least 100 bp of this feature but not the whole feature.</span>", 4787 "# genomic features" : "<span>is the number of genomic features (genes, transcripts, CDS) in the assembly (complete and partial), based on a user-provided annotated list of gene positions in the reference genome. A feature counts as 'partially covered' if the assembly contains at least 100 bp of this feature but not the whole feature.</span>",
4788 "# operons" : "<span>is the number of operons in the assembly (complete and partial), based on a user-provided annotated list of operon positions in the reference genome. An operon counts as 'partially covered' if the assembly contains at least 100 bp of this operon but not the whole operon.</span>", 4788 "# operons" : "<span>is the number of operons in the assembly (complete and partial), based on a user-provided annotated list of operon positions in the reference genome. An operon counts as 'partially covered' if the assembly contains at least 100 bp of this operon but not the whole operon.</span>",
4789 "# predicted genes (unique)" : "<span>is the number of unique genes in the assembly found by a gene prediction tool.</span>", 4789 "# predicted genes (unique)" : "<span>is the number of unique genes in the assembly found by a gene prediction tool.</span>",
4790 "# predicted genes (>= 0 bp)" : "<span>is the number of found genes having length greater than or equal to 0 bp.</span>", 4790 "# predicted genes (>= 0 bp)" : "<span>is the number of found genes having length greater than or equal to 0 bp.</span>",
4791 4791
4792 "Complete BUSCO (%)" : "<span>is the percent of BUSCO (Universal Single-Copy Ortholog) genes found in the assembly in a complete form.</span>",
4793 "Partial BUSCO (%)" : "<span>is the percent of BUSCO (Universal Single-Copy Ortholog) genes found in the assembly in a partial form.</span>",
4794
4792 "Cumulative length" : "<span>plot shows the growth of assembly contig lengths. On the x-axis, contigs are ordered from largest (contig #1) to smallest. The y-axis gives the size of the x largest contigs in the assembly.</span>", 4795 "Cumulative length" : "<span>plot shows the growth of assembly contig lengths. On the x-axis, contigs are ordered from largest (contig #1) to smallest. The y-axis gives the size of the x largest contigs in the assembly.</span>",
4793 "Nx" : "<span>plot shows the Nx metric value as x varies from 0 to 100.</span> <span>Nx is the minimum contig length <b>y</b> such that using contigs of length at least <b>y</b> accounts for at least x% of the total assembly length.</span>", 4796 "Nx" : "<span>plot shows the Nx metric value as x varies from 0 to 100.</span> <span>Nx is the minimum contig length <b>y</b> such that using contigs of length at least <b>y</b> accounts for at least x% of the total assembly length.</span>",
4794 "NGx" : "<span>plot shows the NGx metric value as x varies from 0 to 100.</span> <span>NGx is the minimum contig length <b>y</b> such that using contigs of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>", 4797 "NGx" : "<span>plot shows the NGx metric value as x varies from 0 to 100.</span> <span>NGx is the minimum contig length <b>y</b> such that using contigs of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>",
4795 "NAx" : "<span>plot shows the NAx metric value as x varies from 0 to 100.</span> <span>NAx is computed similarly to Nx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken into aligned blocks at misassembly breakpoints. NAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the assembly. This metric is computed only if a reference genome is provided.</span>", 4798 "NAx" : "<span>plot shows the NAx metric value as x varies from 0 to 100.</span> <span>NAx is computed similarly to Nx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken into aligned blocks at misassembly breakpoints. NAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the assembly. This metric is computed only if a reference genome is provided.</span>",
4796 "NGAx" : "<span>plot shows the NGAx metric value as x varies from 0 to 100.</span><span>NGAx is computed similarly to NGx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken at misassembly breakpoints. NGAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>", 4799 "NGAx" : "<span>plot shows the NGAx metric value as x varies from 0 to 100.</span><span>NGAx is computed similarly to NGx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken at misassembly breakpoints. NGAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>",