# QUAST

Quality Assessment Tool for Genome Assemblies by CAB

 Contigs are ordered from largest (contig #1) to smallest. FRCurve: Y is the total number of aligned bases divided by the reference length, in the contigs having the total number of at most X. Contigs are broken into nonoverlapping 100 bp windows. Plot shows number of windows for each GC percentage. Plot shows number of contigs with GC percentage in a certain range.

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relocations"},{"values":[0,20,9,16,38,19],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,2,2,2,2,4],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[0,18,11,10,33,16],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[0,6548228,4962794,6938326,8168042,4698174],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[0,52,38,35,72,43],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"},{"values":[0,0,0,0,1,0],"quality":"Less is better","isMain":false,"metricName":"# scaffold gap size mis."},{"values":[0,8,16,6,4,10],"quality":"Equal","isMain":false,"metricName":"# possible MGEs"},{"values":[0,0,0,0,0,1],"quality":"Less is better","isMain":false,"metricName":"# unaligned mis. contigs"}]],["Unaligned",[{"values":[0,1,4,5,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,21418,57255,83130,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,20,12,12,40,28],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,97343,95660,87926,136267,154665],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[0,69584,21501,14096,80581,18424],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[0,5794,10756,3603,5926,12360],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[0,93567,59896,64666,63792,72926],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.00","579.50","184.09","118.27","680.43","155.74"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["0.00","48.25","92.09","30.23","50.04","104.48"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[0,4909,10331,2964,4933,12101],"quality":"Less is better","isMain":false,"metricName":" # indels (<= 5 bp)"},{"values":[0,885,425,639,993,259],"quality":"Less is better","isMain":false,"metricName":" # indels (> 5 bp)"},{"values":[0,0,0,100,3386,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","0.00","0.00","0.82","26.93","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Statistics without reference",[{"values":[38,32,77,29,51,49],"quality":"Equal","isMain":true,"metricName":"# contigs"},{"values":[49,32,111,31,51,49],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[42,32,102,30,51,49],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[33,32,61,29,50,45],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 5000 bp)"},{"values":[20,32,34,25,50,36],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 10000 bp)"},{"values":[19,24,21,24,49,26],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 25000 bp)"},{"values":[19,21,20,22,40,25],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 50000 bp)"},{"values":[1524479,1534530,1527374,1084210,857809,1525027],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[12163350,12482519,12283154,12205282,12571691,12382136],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[12175460,12482519,12342374,12207375,12571691,12382136],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[12171581,12482519,12337589,12206923,12571691,12382136],"quality":"More is better","isMain":true,"metricName":"Total length (>= 1000 bp)"},{"values":[12141521,12482519,12217993,12205282,12568023,12363811],"quality":"More is better","isMain":false,"metricName":"Total length (>= 5000 bp)"},{"values":[12056627,12482519,12044022,12177942,12568023,12294679],"quality":"More is better","isMain":true,"metricName":"Total length (>= 10000 bp)"},{"values":[12046383,12327090,11867163,12165776,12543819,12161782],"quality":"More is better","isMain":false,"metricName":"Total length (>= 25000 bp)"},{"values":[12046383,12224573,11840545,12094220,12272413,12129388],"quality":"More is better","isMain":true,"metricName":"Total length (>= 50000 bp)"},{"values":[776910,776810,762979,776728,432306,737373],"quality":"More is better","isMain":false,"metricName":"N50"},{"values":[564006,564467,465562,556525,229910,448848],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[6,6,6,7,11,7],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[11,11,11,12,21,12],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["38.15","38.21","38.46","38.17","38.23","38.15"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["K-mer-based statistics",[{"values":["99.90","64.39","86.31","91.72","62.36","85.46"],"quality":"More is better","isMain":true,"metricName":"K-mer-based completeness"},{"values":["99.39","84.57","90.42","71.44","66.97","78.57"],"quality":"More is better","isMain":false,"metricName":"K-mer-based cor. length (%)"},{"values":["0.00","14.25","6.01","27.88","32.14","19.80"],"quality":"Less is better","isMain":false,"metricName":"K-mer-based mis. length (%)"},{"values":["0.61","1.18","3.57","0.68","0.89","1.63"],"quality":"Less is better","isMain":false,"metricName":"K-mer-based undef. length (%)"},{"values":[0,3,3,7,10,3],"quality":"Less is better","isMain":true,"metricName":"# k-mer-based misjoins"},{"values":[0,3,3,7,8,3],"quality":"Equal","isMain":false,"metricName":" # k-mer-based translocations"},{"values":[0,0,0,0,2,0],"quality":"Equal","isMain":false,"metricName":" # k-mer-based 100kbp relocations"}]],["Predicted genes",[]],["Similarity statistics",[{"values":[0,0,0,0,0,0],"quality":"Equal","isMain":false,"metricName":"# similar correct contigs"},{"values":[0,8,7,9,7,9],"quality":"Equal","isMain":false,"metricName":"# similar misassembled blocks"}]],["Reference statistics",[{"values":[12157105,12157105,12157105,12157105,12157105,12157105],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":[17,17,17,17,17,17],"quality":"Equal","isMain":false,"metricName":"Reference fragments"},{"values":["38.15","38.15","38.15","38.15","38.15","38.15"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"}]]],"assembliesWithNs":["Flye","MaSuRCA"],"referenceName":"Saccharomyces_cerevisiae.R64_1_1.dna.toplevel","date":"03 April 2018, Tuesday, 17:30:19","subreferences":[],"minContig":3000,"order":[0,1,2,3,4,5],"assembliesNames":["UpperBound","Canu","FALCON","Flye","MaSuRCA","Miniasm"]}
{{ qualities }}
{{ mainMetrics }}
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{{ genesInContigs }}
{{ operonsInContigs }}
[{{ num_contigs }}, {{ Largest_alignment }}, {{ Total_aligned_length }}, {{ num_misassemblies }}, {{ Misassembled_contigs_length }}, {{ num_mismatches_per_100_kbp }}, {{ num_indels_per_100_kbp }}, {{ num_N's_per_100_kbp }}, {{ Genome_fraction }}, {{ Duplication_ratio }}, {{ NGA50 }}]
{{ allMisassemblies }}
{{ krona }}
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{ "# contigs" : "is the total number of contigs in the assembly.", "Largest contig" : "is the length of the longest contig in the assembly.", "Total length" : "is the total number of bases in the assembly.", "Reference length" : "is the total number of bases in the reference.", "# contigs (>= 0 bp)" : "is the total number of contigs in the assembly that have size greater than or equal to 0 bp.", "Total length (>= 0 bp)" : "is the total number of bases in the contigs having size greater than or equal to 0 bp.", "N50" : "is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly. Usually there is no value that produces exactly 50%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 50% of the total assembly length.", "NG50" : "is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "N75" : "is the contig length such that using longer or equal length contigs produces 75% of the bases of the assembly. Usually there is no value that produces exactly 75%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 75% of the total assembly length.", "NG75" : "is the contig length such that using longer or equal length contigs produces 75% of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "L50" : "is the minimum number of contigs that produce half (50%) of the bases of the assembly. In other words, it's the number of contigs of length at least N50.", "LG50" : "is the minimum number of contigs that produce half (50%) of the bases of the reference genome. In other words, it's the number of contigs of length at least NG50. This metric is computed only if a reference genome is provided.", "L75" : "is the minimum number of contigs that produce 75% of the bases of the assembly. In other words, it's the number of contigs of length at least N75.", "LG75" : "is the minimum number of contigs that produce 75% of the bases of the reference genome. In other words, it's the number of contigs of length at least NG75. This metric is computed only if a reference genome is provided.", "NA50" : "is N50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "NGA50" : "is NG50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "NA75" : "is N75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "NGA75" : "is NG75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "LA50" : "is L50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "LGA50" : "is LG50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "LA75" : "is L75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "LGA75" : "is LG75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "Average %IDY" : "is the average of alignment identity percent (Nucmer measure of alignment accuracy) among all contigs.", "# misassemblies" : "is the number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (relocation) or they overlap on more than 1 kbp (relocation) or flanking sequences align on different strands (inversion) or different chromosomes (translocation).", "# large block misassemblies" : "is the number of misassemblies between alignments with length greater than or equal to 3 kbp and with the misassembly threshold equal to 5 kbp (instead of default 1 kbp for regular misassemblies).", "# misassembled contigs" : "is the number of contigs that contain misassembly events.", "Misassembled contigs length" : "is the number of total bases contained in all contigs that have one or more misassemblies.", "# relocations" : "is the number of relocation events among all misassembly events. Relocation is a misassembly where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference, or they overlap by more than 1 kbp and both flanking sequences align on the same chromosome.", "# translocations" : "is the number of translocation events among all misassembly events. Translocation is a misassembly where the flanking sequences align on different chromosomes.", "# interspecies translocations" : "is the number of interspecies translocation events among all misassembly events. Interspecies translocation is a misassembly where the flanking sequences align on different references (based on alignments to the combined reference).", "# inversions" : "is the number of inversion events among all misassembly events. Inversion is a misassembly where it is not a relocation and the flanking sequences align on opposite strands of the same chromosome.", "# large relocations" : "is the number of relocation events among all large block misassemblies. Relocation is a misassembly where the left flanking sequence aligns over 5 kbp away from the right flanking sequence on the reference, or they overlap by more than 5 kbp and both flanking sequences align on the same chromosome.", "# large translocations" : "is the number of translocation events among all large block misassemblies. Translocation is a misassembly where the flanking sequences align on different chromosomes.", "# large i/s translocations" : "is the number of interspecies translocation events among all large block misassemblies. Interspecies translocation is a misassembly where the flanking sequences align on different references (based on alignments to the combined reference).", "# large inversions" : "is the number of inversion events among all large block misassemblies. Inversion is a misassembly where it is not a relocation and the flanking sequences align on opposite strands of the same chromosome.", "# local misassemblies" : "is the number of local misassemblies. We define a local misassembly breakpoint as a breakpoint that satisfies these conditions:
1. Two or more distinct alignments cover the breakpoint.
2. The gap between left and right flanking sequences is less than 1 kbp.
3. The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.
", "# scaffold gap size mis." : "is the number of scaffold gap size misassemblies. We define scaffold gap size misassembly as a breakpoint where the flanking sequences combined in scaffold on the wrong distance. These misassemblies are not included in the total number of misassemblies. ", "# possibly misassembled contigs": "is the number of contigs that contain large unaligned fragment (default min length is 500 bp) and thus could possibly contain interspecies translocation with unknown reference.", "# possible misassemblies" : "is the number of putative interspecies translocations in possibly misassembled contigs if each large unaligned fragment is supposed to be a fragment of unknown reference.", "# intergenomic misassemblies" : "is the number of all found and putative (possible) interspecies translocations.", "# structural variations" : "is the number of misassemblies matched with structural variations.", "# possible MGEs" : "is the number of misassemblies possibly caused by mobile genetic elements (MGE). We define a possible MGE as an event that satisfies these conditions:
1. There is two misassemblies of the same type around a short alignment (less than 6 kbp)
2. The gap between two long flanking sequences on the sides of the short alignment is less than 6 kbp.
3. The long flanking sequences both are on the same strand of the same chromosome of the reference genome.