RNA-Quast contents for Homo sapiens + EBOV 7h



S5.1: Short report for Homo sapiens + EBOV 7h assemblies

back to top

METRICS/TRANSCRIPTSGenesAvg. number of exons per isoformTranscriptsTranscripts > 500 bpTranscripts > 1000 bpAlignedUniquely alignedMultiply alignedUnalignedAvg. aligned fractionAvg. alignment lengthAvg. mismatches per transcriptMisassembliesDatabase coverage
Trinity579925.97112157550409313191214041165187641710.9831040.8751.74612940.178
Trans-ABySS579925.971275008697173741027423326391328387750.982534.4020.75347690.21
Oases579925.971259024163070115596257703229396169413210.921364.3772.515188930.201
SOAPdenovo-Trans579925.971165909291351525116540116277717385080.995455.9590.4431250.158
IDBA-Tran579925.97195730371351618195623942395951070.992697.7480.8342030.15
Bridger579925.9711032844027623487103098967375291860.975866.6081.48725090.141
BinPacker579925.971288882680922928288402508658480.9382505.4263.67426490.102
Shannon579925.97113319956849357851330321258397861670.981918.8541.42626050.167
rnaSPAdes579925.9712436043954821867241562236219180620420.987470.1611.06712190.173
SPAdes 57992 5.971 125233 31264 15598 124551 110918 7690 682 0.986 489.2 0.72 2042 0.143
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
Trinity984939721133849991433246961682358890.5140.461335925820136579474980.473
Trans-ABySS1037736941205351571763440042245857680.4640.450018117092797031280190.42
Oases1025841281135552521780151152031965490.5390.4919613214076767696604260.561
SOAPdenovo-Trans940631161123439651116632251401841060.3850.334178016185250736856810.372
IDBA-Tran8675776111032003108007801485520120.4510.38253504857439613350890.508
Bridger84802722990332861055929651258735560.4350.391235854418729804406080.44
BinPacker672825857054287984002851879631640.6780.65418234218271227111730.805
Shannon888925621074737611295729641616743540.5290.456415338102758664381690.609
rnaSPAdes1018636281207846911279538501583749810.4110.362396760734413121592510.249
SPAdes 9154 2790 10454 3454 10453 2795 12569 3461 0.422 0.377 18444 47018 35929 61658 0.319



S5.2: Assembly completeness (sensitivity, true positive rate) for Homo sapiens + EBOV 7h assemblies

back to top

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
Trinity0.1781.7571.992984939721133849991433246961682358891346221165980.4610.5140.9010.5020.38233592
Trans-ABySS0.211.6632.5881037736941205351571763440042245857681473521215890.40.4640.8580.4410.31350018
Oases0.2014.3474.4741025841281135552521780151152031965491382181192760.4910.5390.8920.5350.42396132
SOAPdenovo-Trans0.1581.061.78940631161123439651116632251401841061312851111170.3340.3850.8490.3450.23117801
IDBA-Tran0.151.0071.6418675776111032003108007801485520121232931042420.380.4510.8850.3950.27125350
Bridger0.1411.4511.7188480272299033286105592965125873556115102988720.3910.4350.8740.4050.28923585
BinPacker0.1021.8841.9356728258570542879840028518796316490688832680.6540.6780.9490.7230.62518234
Shannon0.1671.9542.769888925621074737611295729641616743541288021104470.4560.5290.8970.5230.39641533
rnaSPAdes0.1731.1611.7311018636281207846911279538501583749811347531145860.360.4110.860.3720.25923967
SPAdes0.1431.0131.625915427901045434541045327951256934611203391027820.3770.4220.8720.3860.26618444



S5.3: Assembly specificity (true negative rate) for Homo sapiens + EBOV 7h assemblies

back to top

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
Trinity4749858201365790.4730.8870.8880.8469201378534029834
Trans-ABySS128019117092797030.420.8860.8860.84510263705846845018
Oases60426140767676960.5610.6620.6630.63925670429493474361
SOAPdenovo-Trans8568161852507360.3720.8950.8910.8544943926827545660
IDBA-Tran3508948574396130.5080.9060.9040.8644444992622852976
Bridger4060844187298040.440.8250.8260.7866042556529842233
BinPacker117321827122710.8050.8480.8510.8215655618512684910
Shannon3816981027586640.6090.8980.8980.8679585726326695013
rnaSPAdes15925160734413120.2490.8230.820.7665900622256571206
SPAdes6165847018359290.3190.880.880.844254776630409751



S5.4: Various comparison and single plots for Homo sapiens + EBOV 7h assemblies

back to top

Various comparison and single plots for Homo sapiens + EBOV 7h 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