RNA-Quast contents for Homo sapiens simulated



S5.1: Short report for Homo sapiens simulated 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
Trinity31196.9913484107178451134541321412300.9892261.3321.2311390.461
Trans-ABySS31196.99252721146067032515024896391220.994939.3120.4591170.535
Oases31196.994646934981281434604941196484200.9592090.552.10540940.592
SOAPdenovo-Trans31196.9914965627042631479214692181730.9941009.080.308490.406
IDBA-Tran31196.991215156422740121341209911170.998859.9660.09680.382
Bridger31196.99104577180516710307953771500.9831581.2991.6525330.346
BinPacker31196.9913415985874241325212174101630.9811755.1551.8497850.372
Shannon31196.99725537292341719670357590.9961061.0130.394660.189
rnaSPAdes31196.99117669116605311744113067220.9681649.1471.823510.431
SPAdes 3119 6.99 10537 4309 2623 10503 10347 87 34 0.995 979.981 0.215 50 0.367
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
Trinity247819152644209646542898500332540.8060.7596829127975462960.864
Trans-ABySS268020742903248559922877696637850.6740.60286002450816312820.927
Oases262318652812205261062995678035250.7370.6822127438562165125850.84
SOAPdenovo-Trans236513802719175536301679439921450.6060.5313567142519194240.907
IDBA-Tran2494570273311583896577476012030.5910.512459912072828060.934
Bridger224713532427152733621570372517860.6550.61440092874556340.884
BinPacker230014022480157937011660408619070.6590.6146344117615451620.87
Shannon1441854162195419201056218311810.6580.59925987005460680.931
rnaSPAdes260617602686202545572220484825960.7170.6786088109555031370.875
SPAdes 2537 1566 2624 1772 3668 1625 4054 1865 0.576 0.538 2863 10295 7030 44 0.919



S5.2: Assembly completeness (sensitivity, true positive rate) for Homo sapiens simulated 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
Trinity0.4612.1542.1752478191526442096465428985003325425771241450.7590.8060.9650.7980.7216829
Trans-ABySS0.5351.5722.3872680207429032485599228776966378531540279740.6020.6740.9380.6660.5518600
Oases0.5924.8544.5272623186528122052610629956780352529821265670.6820.7370.9450.7330.61821274
SOAPdenovo-Trans0.4061.2741.9522365138027191755363016794399214524266213840.5310.6060.9140.570.4493567
IDBA-Tran0.3821.0131.50424945702733115838965774760120324449203460.5120.5910.9230.5230.3814599
Bridger0.3461.5071.6432247135324271527336215703725178621962198810.610.6550.9330.6140.4974400
BinPacker0.3721.9491.9362300140224801579370116604086190723036208120.6140.6590.9350.6240.516344
Shannon0.1891.4372.0741441854162195419201056218311811063792250.5990.6580.9040.6330.5032598
rnaSPAdes0.4311.5351.6982606176026862025455722204848259625828239010.6780.7170.9530.6880.6086088
SPAdes0.3671.0121.4052537156626241772366816254054186524554216270.5380.5760.9180.5310.412863



S5.3: Assembly specificity (true negative rate) for Homo sapiens simulated 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
Trinity961279754620.8640.8450.8550.785255489154852934
Trans-ABySS8224508163120.9270.9150.930.845216495682007979
Oases58538562165120.840.7760.7830.737398358017472494
SOAPdenovo-Trans241425191940.9070.8820.8940.814133207721669839
IDBA-Tran61207282800.9340.9490.9730.8589968961477422
Bridger34928745560.8840.860.8750.784134053992221251
BinPacker621176154510.870.8310.8440.767186518183621382
Shannon8700546060.9310.9120.930.8326996209526628
rnaSPAdes371095550310.8750.8790.8920.806170155122185138
SPAdes441029570300.9190.9160.9340.8359561201920540



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

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Various comparison and single plots for Homo sapiens simulated 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