RNA-Quast contents for Homo sapiens + EBOV 3h



S5.1: Short report for Homo sapiens + EBOV 3h 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
Trinity579925.97196550417792715496414921545541360.9821083.5551.72815800.163
Trans-ABySS579925.971227117560233076722626421399821518530.974517.9160.70479560.19
Oases579925.9712184831414169819621752418694012249590.9251308.2162.383248450.185
SOAPdenovo-Trans579925.971132751236021311013219213011913605590.993464.3680.4291480.145
IDBA-Tran579925.9717508729737135087501674003402710.992718.4020.7991780.137
Bridger579925.97182495328532043482359776994411360.978925.6191.4318530.135
BinPacker579925.971188518061646187614891390.9082899.3926.1842790.006
Shannon579925.971103815454232824810372998368565860.982921.0461.31321610.149
rnaSPAdes579925.9711974773009017195195967191228154315100.986462.0871.0019430.16
SPAdes 57992 5.971 85257 23614 12775 85001 79356 1612 256 0.983 661.322 0.944 1262 0.132
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
Trinity923832751068741621298638261521648330.5180.464304455386836225312710.555
Trans-ABySS969729711133941441515031531967044800.4440.384420511237375135887700.49
Oases962232651075543031627839481865652110.5490.4989519413179069556378160.645
SOAPdenovo-Trans87092481105623195993225531258232840.3830.332162175886049648611150.441
IDBA-Tran804156910360163996815691322116420.4540.381230254537138273220790.602
Bridger82442540966430661002027811190733270.4550.408220244271130697273690.529
BinPacker4532274582355502555562640.7180.71213761269595860.769
Shannon814720471003930181116823031410434030.5240.45356837197856189224750.698
rnaSPAdes960431731137041291144233351413443380.4070.3542035858962428601205520.298
SPAdes 8849 2650 9988 3126 9529 2653 11049 3132 0.451 0.407 15761 35654 27474 39000 0.41



S5.2: Assembly completeness (sensitivity, true positive rate) for Homo sapiens + EBOV 3h 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
Trinity0.1631.6971.972923832751068741621298638261521648331281361108690.4640.5180.90.5130.39330445
Trans-ABySS0.191.5542.54969729711133941441515031531967044801396921144810.380.4440.850.4260.29644205
Oases0.1853.914.409962232651075543031627839481865652111318421133300.4980.5490.8960.5540.43495194
SOAPdenovo-Trans0.1451.0421.76987092481105623195993225531258232841252341059270.3320.3830.850.3490.23616217
IDBA-Tran0.1371.0051.62680415691036016399681569132211642117962996750.3810.4540.8860.4070.28323025
Bridger0.1351.4341.7398244254096643066100202781119073327114436987940.4080.4550.8840.4350.31622024
BinPacker0.0062.0141.906453227458235550255556264589255020.7120.7180.9540.7680.6881376
Shannon0.1491.8082.71814720471003930181116823031410434031213491038690.450.5240.8960.5280.39635683
rnaSPAdes0.161.1171.742960431731137041291144233351413443381299171104250.3540.4070.860.3710.25920358
SPAdes0.1321.0031.5228849265099883126952926531104931321157881009100.4070.4510.8880.4270.3115761



S5.3: Assembly specificity (true negative rate) for Homo sapiens + EBOV 3h 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
Trinity3127153868362250.5550.90.9020.8638156055422483031
Trans-ABySS88770112373751350.490.8970.8970.8638694517031103940
Oases37816131790695560.6450.7440.7460.72221248604056575335
SOAPdenovo-Trans6111558860496480.4410.9190.9180.8834455639818078864
IDBA-Tran2207945371382730.6020.9340.9340.94052529613761951
Bridger2736942711306970.5290.8710.8730.8375703993619121282
BinPacker8612695950.7690.7920.7960.76336833251407637
Shannon2247571978561890.6980.9160.9180.8917904534416515061
rnaSPAdes12055258962428600.2980.8610.860.8095264960839153267
SPAdes3900035654274740.410.8960.8970.8613889044519068858



S5.4: Various comparison and single plots for Homo sapiens + EBOV 3h assemblies

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Various comparison and single plots for Homo sapiens + EBOV 3h 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