RNA-Quast contents for Escherichia coli



S5.1: Short report for Escherichia coli 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
Trinity44971.0154403108034741734074172300.99467.0350.368130.334
Trans-ABySS44971.01595551273446916389921153920.98310.4420.322180.043
Oases44971.0157364197474371396921262250.988457.7170.7061030.334
SOAPdenovo-Trans44971.0157007123043968486799311590.994364.8810.13410.225
IDBA-Tran44971.015380311994143757373215460.996540.8280.16700.183
Bridger44971.0154254111836340483883162060.991472.8060.265520.319
BinPacker44971.01515710966151126560.9471100.7742.05180.009
Shannon44971.0154221112337240393885101820.993482.6590.185540.318
rnaSPAdes44971.0157067114234068706821211970.992359.1950.212100.208
SPAdes 4497 1.015 4119 1333 489 3984 3893 33 135 0.988 558.904 0.248 12 0.16
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
Trinity950396143559695039614355960.6470.509335816193030.746
Trans-ABySS9632126389632126380.2160.191100172474940.113
Oases916414140859591641414085950.5810.452502924928820.674
SOAPdenovo-Trans5872618243115872618243110.4470.3732941181432880.411
IDBA-Tran5502506992945502506992940.5070.45154375916730.396
Bridger920382137656292038213765620.6360.507321215502730.749
BinPacker47344736473447360.7280.719322530.272
Shannon907393135056590739313505650.6360.509320515352550.751
rnaSPAdes4691877072374691877072370.420.3452687175635110.38
SPAdes 503 210 591 242 503 210 591 242 0.478 0.436 1292 638 2075 0.322



S5.2: Assembly completeness (sensitivity, true positive rate) for Escherichia coli 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
Trinity0.3341.0121.746950396143559695039614355969594000.5090.6470.6490.6540.272
Trans-ABySS0.0431.0441.35396321263896321263899320.1910.2160.2190.1050.031
Oases0.3341.4432.454916414140859591641414085959304200.4520.5810.5830.5640.239
SOAPdenovo-Trans0.2251.0021.5985872618243115872618243115942650.3730.4470.4490.3680.139
IDBA-Tran0.1831.0011.325502506992945502506992945562540.450.5070.5090.4420.187
Bridger0.3191.0141.701920382137656292038213765629293860.5070.6360.6380.640.262
BinPacker0.0091.2671.277473447364734473647340.7190.7280.7280.7230.554
Shannon0.3181.0271.713907393135056590739313505659143960.5090.6360.6370.6320.265
rnaSPAdes0.2081.0091.5644691877072374691877072374771920.3450.420.4230.330.111
SPAdes0.161.0061.2775032105912425032105912425092130.4360.4780.4810.3970.164



S5.3: Assembly specificity (true negative rate) for Escherichia coli 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
Trinity303335816190.7460.8060.8810.4391396466553311
Trans-ABySS749410017240.1130.6430.6210.461850602782497
Oases882502924920.6740.7310.7820.41519910001260107
SOAPdenovo-Trans3288294118140.4110.7950.8280.5199321461595296
IDBA-Tran167315437590.3960.7160.7420.3727563251299897
Bridger273321215500.7490.7950.8690.4321338116535978
BinPacker533220.2720.3840.370.1348781109362
Shannon255320515350.7510.7990.8730.4221350719552664
rnaSPAdes3511268717560.380.7860.8080.5368665051628649
SPAdes207512926380.3220.6930.7080.3716655551588418



S5.4: Various comparison and single plots for Escherichia coli assemblies

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Various comparison and single plots for Escherichia coli 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