RNA-Quast contents for Homo sapiens + EBOV 23h



S5.1: Short report for Homo sapiens + EBOV 23h 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
Trinity579925.97197849424972778597647940465492020.9841143.4921.68410660.161
Trans-ABySS579925.971213005582133286621204420494719999610.984578.8810.76932530.188
Oases579925.9711784981149768353017774716131310487510.9371500.7762.311111940.176
SOAPdenovo-Trans579925.971131711246361341813078912889612639220.995482.2570.468940.143
IDBA-Tran579925.97178116315001419677999770594071170.993725.580.8661340.136
Bridger579925.97183744335782056083546790214041980.977929.8571.4318440.131
BinPacker579925.971122911183410862122741043719170.9293072.8983.75514360.048
Shannon579925.9718445627820150078437382753421830.994703.7480.5833810.116
rnaSPAdes579925.9712061333269718629203335199122149627980.987476.1761.159080.159
SPAdes 57992 5.971 93814 25204 13245 87567 81873 1707 6247 0.984 649.419 0.951 1206 0.126
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
Trinity894734861032942991262340651476549910.5150.462300095194933810336960.524
Trans-ABySS946732921100044341547535751949349430.4610.401435859961770234908400.462
Oases916635791016744511517643301720854570.5510.5047368610948357036350150.623
SOAPdenovo-Trans85822667102513404997927491250335120.3850.335160665506846001609130.419
IDBA-Tran796471010120174497647141325317550.4510.382231744365736242246790.559
Bridger7837249291922981961627361142132460.4440.399210884039628362290470.492
BinPacker305413533115141537941523387415910.7190.7078375946248362020.83
Shannon6519150282622188830916311090023690.4730.402238795603648039233780.658
rnaSPAdes928333631102042171132635351392244400.4030.3542142956981401351286670.277
SPAdes 8232 2650 9329 3034 9031 2654 10517 3039 0.439 0.398 15644 33929 25755 42074 0.379



S5.2: Assembly completeness (sensitivity, true positive rate) for Homo sapiens + EBOV 23h 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
Trinity0.1611.8061.985894734861032942991262340651476549911270551107200.4620.5150.9030.5070.39330009
Trans-ABySS0.1881.6442.5946732921100044341547535751949349431373031143990.4010.4610.8610.4420.32243585
Oases0.1763.974.024916635791016744511517643301720854571284511119200.5040.5510.9020.5530.44473686
SOAPdenovo-Trans0.1431.0491.7785822667102513404997927491250335121240801055490.3350.3850.8550.3490.23816066
IDBA-Tran0.1361.0061.62279647101012017449764714132531755117223996870.3820.4510.8870.4010.28223174
Bridger0.1311.4591.733783724929192298196162736114213246111190961870.3990.4440.8810.4210.30821088
BinPacker0.0482.092.0083054135331151415379415233874159145571426320.7070.7190.9590.7780.7018375
Shannon0.1161.4352.33865191502826221888309163110900236997773827080.4020.4730.8760.4620.33723879
rnaSPAdes0.1591.1471.724928333631102042171132635351392244401288221100400.3540.4030.860.3660.25721429
SPAdes0.1261.0041.509823226509329303490312654105173039110419963680.3980.4390.8860.410.29715644



S5.3: Assembly specificity (true negative rate) for Homo sapiens + EBOV 23h 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
Trinity3369651949338100.5240.9030.9040.8678556962425921755
Trans-ABySS9084099617702340.4620.9020.9020.8649098959734004255
Oases35015109483570360.6230.7670.7670.74320552094958122773
SOAPdenovo-Trans6091355068460010.4190.9040.9010.8684420473020148614
IDBA-Tran2467943657362420.5590.9160.9150.8794032516816753602
Bridger2904740396283620.4920.8560.8570.8215621510822305397
BinPacker202946248360.830.8550.8580.831293950956378279
Shannon2337856036480390.6580.9530.9540.9294882810410803470
rnaSPAdes12866756981401350.2770.8470.8450.7955351652544975343
SPAdes4207433929257550.3790.880.8790.8443715173521824374



S5.4: Various comparison and single plots for Homo sapiens + EBOV 23h assemblies

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Various comparison and single plots for Homo sapiens + EBOV 23h 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