RNA-Quast contents for Candida albicans



S5.1: Short report for Candida albicans 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
Trinity128671.0758970557834178786500035651840.994969.3271.819720.511
Trans-ABySS128671.075263561330479792592814459106674280.988773.5841.2884490.653
Oases128671.07524818163719813241921455683996260.986941.62.1216130.604
SOAPdenovo-Trans128671.075149275424276914724760670732030.997567.1690.56990.564
IDBA-Tran128671.0759408571129499238572534841700.996922.0960.80780.527
Bridger128671.0758413615940388226485327961870.9871131.3261.9962360.476
BinPacker128671.0758324648542678138490526101860.9851189.5522.2832590.47
Shannon128671.075172258567407717071857372821540.993678.9470.9993620.541
rnaSPAdes128671.0758297561439398092484729612050.9881171.7141.959820.508
SPAdes 12867 1.075 6821 4858 3504 6502 3983 2393 319 0.99 1279.411 1.799 60 0.485
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
Trinity530241466011458553024146601145850.8170.746748835295910.799
Trans-ABySS673452147833588467345214783358840.8320.748209371074525590.765
Oases642548087237545064254808723754500.8190.74919840956816530.789
SOAPdenovo-Trans536232906742452253623290674245220.7560.62912185759617060.775
IDBA-Tran538032386229400353803238622940030.7710.687799835955740.786
Bridger513640055581432251364005558143220.8090.76653725875020.771
BinPacker516240335556434351624033555643430.820.776637023134950.761
Shannon547537366884456254753736688445620.7710.661464088736040.867
rnaSPAdes541345335819478354134533581947830.8490.806622522068840.708
SPAdes 5266 4437 5529 4542 5266 4437 5529 4542 0.852 0.822 5246 1793 568 0.732



S5.2: Assembly completeness (sensitivity, true positive rate) for Candida albicans 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
Trinity0.5111.0391.52653024146601145855302414660114585570245340.7460.8170.8260.8130.624
Trans-ABySS0.6531.9163.43867345214783358846734521478335884727757500.7480.8320.840.8410.637
Oases0.6042.253.29164254808723754506425480872375450689952640.7490.8190.8270.8220.623
SOAPdenovo-Trans0.5641.0072.14753623290674245225362329067424522582637300.6290.7560.7660.7580.513
IDBA-Tran0.5271.0031.48653803238622940035380323862294003574236310.6870.7710.7810.7740.507
Bridger0.4761.1051.39651364005558143225136400555814322553644010.760.8090.8180.8010.625
BinPacker0.471.1361.38651624033555643435162403355564343556144320.7760.820.8290.8160.643
Shannon0.5411.4122.5154753736688445625475373668844562596642140.660.7710.7830.7740.517
rnaSPAdes0.5081.0591.38554134533581947835413453358194783580249120.8060.8490.8570.8510.702
SPAdes0.4851.0011.22652664437552945425266443755294542564248000.8220.8520.860.8530.703



S5.3: Assembly specificity (true negative rate) for Candida albicans 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
Trinity591748835290.7990.7880.8470.4696102732283605
Trans-ABySS255920937107450.7650.7990.8490.52226625795440753
Oases16531984095680.7890.7910.8410.504246089795546400
SOAPdenovo-Trans17061218575960.7750.8510.8950.592102853842118354
IDBA-Tran574799835950.7860.790.8590.4295704252191265
Bridger502653725870.7710.7440.8070.39495244692567861
BinPacker495637023130.7610.7250.7890.36596640942709599
Shannon6041464088730.8670.8620.9110.592138328412069267
rnaSPAdes884622522060.7080.6980.7570.3797370113118082
SPAdes568524617930.7320.7280.7920.36987882502600043



S5.4: Various comparison and single plots for Candida albicans assemblies

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Various comparison and single plots for Candida albicans 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