RNA-Quast contents for Homo sapiens



S5.1: Short report for Homo sapiens assemblies

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METRICS/TRANSCRIPTSGenesAvg. number of exons per isoformTranscriptsTranscripts > 500 bpTranscripts > 1000 bpAlignedUniquely alignedMultiply alignedUnalignedAvg. aligned fractionAvg. alignment lengthAvg. mismatches per transcriptMisassembliesDatabase coverage
Trinity579925.971365427113994640613303663178802514350610.992795.2251.38233780.216
Trans-ABySS579925.97117624391513625977916066961576053188091557430.992246.8460.57327430.282
Oases579925.97113161434794142074741209240858267105711069030.884343.4791.2532161270.083
SOAPdenovo-Trans579925.9711087869655132752910083169949208998795530.996218.00.2692790.103
IDBA-Tran579925.97128137171446235162594912558552087218800.997487.1060.6663020.09
Bridger579925.97127789292081432012550222306961530228700.99654.4131.43973290.074
BinPacker579925.9712795726426226112770920274432480.9692335.7294.62956030.055
Shannon579925.97116248654363313281503241402161451121620.992711.8311.26228370.008
rnaSPAdes579925.971668019112806498606320836115854264359360.99412.2381.24951260.118
SPAdes 57992 5.971 353728 82573 31039 332617 303526 18281 21111 0.994 410.224 0.803 2022 0.086
METRICS/TRANSCRIPTS50%-assembled genes95%-assembled genes50%-covered genes95%-covered genes50%-assembled isoforms95%-assembled isoforms50%-covered isoforms95%-covered isoformsMean isoform coverageMean isoform assemblyPredicted genes50%-matched95%-matchedUnannotatedMean fraction of transcript matched
Trinity1131352281293164972078067882470985480.5050.456457495985497951938000.284
Trans-ABySS12672589615579845927440682440372109100.4790.3828331223206415746712723630.145
Oases42067915541147076058681258417180.3320.268184371133920517466742470.144
SOAPdenovo-Trans643521107760249480912264990726840.2650.2313320763948483079050500.065
IDBA-Tran6471709788410867734709984610870.350.3113793735324274912035690.142
Bridger530818565818202867252105739023100.3310.3124002526146154061867730.114
BinPacker412123584159244261702824625429520.6980.689186361712472918600.769
Shannon934242119530696424212523070.2840.25221295447622631284620.037
rnaSPAdes86953046978135401107732531268137800.3690.3394788638308219425514120.063
SPAdes 6626 1747 7556 2115 7725 1755 9207 2124 0.337 0.306 33968 33552 24135 268461 0.091



S5.2: Assembly completeness (sensitivity, true positive rate) for Homo sapiens assemblies

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From the RNA-Quast manual page: "Assembly completeness (sensitivity). For the following metrics (calculated with reference genome and gene database) rnaQUAST attempts to select best-matching database isoforms for every transcript. Note that a single transcript can contribute to multiple isoforms in the case of, for example, paralogous genes or genomic repeats. At the same time, an isoform can be covered by multiple transcripts in the case of fragmented assembly or duplicated transcripts in the assembly." For further details see the RNA-Quast manual.

METRICS/TRANSCRIPTSDatabase coverageDuplication ratioAvg. number of transcripts mapped to one isoform50%-assembled genes95%-assembled genes50%-covered genes95%-covered genes50%-assembled isoforms95%-assembled isoforms50%-covered isoforms95%-covered isoforms50%-assembled exons95%-assembled exonsMean isoform assemblyMean isoform coverageMean exon coverageAvg. percentage of isoform 50%-covered exonsAvg. percentage of isoform 95%-covered exonsGeneMarkS-T genes
Trinity0.2162.3962.4351131352281293164972078067882470985481485291271090.450.5050.8890.4920.37664574
Trans-ABySS0.2821.7433.54912672589615579845927440682440372109101817641412780.3820.4790.8320.450.30583312
Oases0.0832.3554.113420679155411470760586812584171862074415440.2680.3320.6930.3030.18184371
SOAPdenovo-Trans0.1031.1871.7756435211077602494809122649907268475853595540.2310.2650.6810.2160.13133207
IDBA-Tran0.091.0121.45564717097884108677347099846108773200564460.3110.350.7990.30.18237937
Bridger0.0741.7081.5795308185658182028672521057390231056402469810.3120.3310.780.2930.20140025
BinPacker0.0552.3892.2444121235841592442617028246254295250898474000.6890.6980.9530.7350.65718636
Shannon0.0081.531.91493424211953069642421252307475424860.2520.2840.5870.2320.11621295
rnaSPAdes0.1181.1921.515869530469781354011077325312681378093214792480.3390.3690.8240.3280.23647886
SPAdes0.0861.0151.456626174775562115772517559207212469623550910.3060.3370.7820.2950.18733968



S5.3: Assembly specificity (true negative rate) for Homo sapiens assemblies

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From the RNA-Quast manual page: "Assembly specificity. To compute the following metrics we use only transcripts that have at least one significant alignment and are not misassembled." For further details see the RNA-Quast manual.

METRICS/TRANSCRIPTSUnannotated50%-matched95%-matchedMean fraction of transcript matchedMean fraction of block matched50%-matched blocks95%-matched blocksMatched lengthUnmatched length
Trinity19380095985497950.2840.880.880.815152502879107403504
Trans-ABySS12723632320641574670.1450.8360.8290.753144521575259867277
Oases674247133920517460.1440.4580.4560.42357768187309215650
SOAPdenovo-Trans90505063948483070.0650.7150.7040.64336169048186722461
IDBA-Tran20356935324274910.1420.7750.7620.69726904419100724455
Bridger18677326146154060.1140.640.6380.57537009197119121516
BinPacker8601712472910.7690.8460.850.7923898269210423707
Shannon128462447622630.0370.1710.1650.111368073199519366
rnaSPAdes55141238308219420.0630.650.6420.56641411984218476750
SPAdes26846133552241350.0910.70.6890.6225750931133487482



S5.4: Various comparison and single plots for Homo sapiens assemblies

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Various comparison and single plots for Homo sapiens assemblies. For detailed descriptions of each plot please check the RNA-Quast manual page:

alignment_multiplicitymismatch_rate

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes
x-covered_exonsblocks_per_alignment

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes
NAxx-assembled_exons

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes
block_lengthx-covered

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes
x-matchedtranscript_length

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes
Nxx-aligned

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes
x-assembledx-matched_blocks

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes
alignments_per_isoform

Single plots: Trinity | Oases | Trans-ABySS | SOAPdenovo-Trans | Bridger | BinPacker | IDBA-Tran | Shannon | SPAdes | rnaSPAdes