RNA-Quast contents for Arabidopsis thaliana



S5.1: Short report for Arabidopsis thaliana 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
Trinity328335.8133461721969133573443232388441850.993978.2131.31512120.298
Trans-ABySS328335.81366004317631971465463564601765410.979745.0880.61272270.334
Oases328335.8135780947279326475744148302663680.9881232.6883.47168040.321
SOAPdenovo-Trans328335.8135087617326870950525502891193510.997561.7460.099510.299
IDBA-Tran328335.81332447181479577323663202054810.998848.3560.1362010.289
Bridger328335.8133001720235128822982225907451950.99990.3492.42719950.256
BinPacker328335.813591454583775589139458230.9761312.1715.90212330.047
Shannon328335.8132768518623120182747825912372070.9961044.9040.7247690.245
rnaSPAdes328335.8133695318068111603662835821913250.995807.4220.3415050.3
SPAdes 32833 5.813 29929 17390 11171 29691 27985 62 238 0.993 944.388 0.43 1189 0.279
METRICS/TRANSCRIPTS50%-assembled genes95%-assembled genes50%-covered genes95%-covered genes50%-assembled isoforms95%-assembled isoforms50%-covered isoforms95%-covered isoformsMean isoform coverageMean isoform assembly50%-matched95%-matchedUnannotatedMean fraction of transcript matched
Trinity1245921961438825421330423021526626510.6840.62530436267638870.92
Trans-ABySS1375518811566022001528319601733422980.6390.582503424181130660.866
Oases1395525991468028121586127531668629810.7340.70746508392387880.933
SOAPdenovo-Trans1145712131535717701147012131539517700.5910.489445554215024790.887
IDBA-Tran1267211751496316421269411751501716420.6540.57930039281428010.929
Bridger1130118611251920761181419091304721270.6660.62324213210178760.911
BinPacker25894772609488270648927295000.7510.74538082929230.917
Shannon1116819621220721031160620041265821470.6980.65724594222748540.929
rnaSPAdes1293122331513626071305122371528326130.6720.603327842899519380.896
SPAdes 12496 2318 13998 2570 12509 2318 14031 2570 0.681 0.632 25910 22414 1100 0.902



S5.2: Assembly completeness (sensitivity, true positive rate) for Arabidopsis thaliana 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 exons
Trinity0.2981.1281.51712459219614388254213304230215266265191985669500.6250.6840.8930.7360.42
Trans-ABySS0.3341.3412.14213755188115660220015283196017334229899841713800.5820.6390.8680.6860.377
Oases0.3211.9762.31813955259914680281215861275316686298196063715170.7070.7340.9040.7950.477
SOAPdenovo-Trans0.2991.0081.96311457121315357177011470121315395177094715652840.4890.5910.8580.630.329
IDBA-Tran0.2891.011.48112672117514963164212694117515017164294428685430.5790.6540.890.7070.384
Bridger0.2561.0671.37211301186112519207611814190913047212781178594930.6230.6660.8870.7150.407
BinPacker0.0471.1491.203258947726094882706489272950015632117370.7450.7510.9110.8180.489
Shannon0.2451.1851.49911168196212207210311606200412658214777697570860.6570.6980.8940.7550.427
rnaSPAdes0.31.0271.60812931223315136260713051223715283261395185694770.6030.6720.8890.7210.404
SPAdes0.2791.0071.40612496231813998257012509231814031257089800667750.6320.6810.8950.7330.419



S5.3: Assembly specificity (true negative rate) for Arabidopsis thaliana 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
Trinity88730436267630.920.9610.9630.94300130451997896
Trans-ABySS306650342418110.8660.960.9610.938399855502854902
Oases78846508392380.9330.9560.9590.937566145583847059
SOAPdenovo-Trans247944555421500.8870.9660.9630.95269026131538113
IDBA-Tran80130039281420.9290.9750.9760.96260938031200078
Bridger87624213210170.9110.9620.9640.943243866841678489
BinPacker23380829290.9170.9420.9450.9184857682495914
Shannon85424594222740.9290.9710.9730.955259181511383207
rnaSPAdes193832784289950.8960.9680.9720.944274577431771614
SPAdes110025910224140.9020.9650.9690.94250386901699469



S5.4: Various comparison and single plots for Arabidopsis thaliana assemblies

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Various comparison and single plots for Arabidopsis thaliana 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