RNA-Quast contents for Mus musculus



S5.1: Short report for Mus musculus 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
Trinity457926.26263305309762180462410605593108950.9931216.8630.845640.208
Trans-ABySS457926.262135402471572971913460513207810987970.995752.8110.3166120.244
Oases457926.26224319610031451832240548177880238226480.891406.0840.625526680.024
SOAPdenovo-Trans457926.2621017452064812603100986998166867590.997519.9620.163610.1
IDBA-Tran457926.26255639230401229455367548842892720.998811.990.187410.096
Bridger457926.26254182271271826653312477851618700.9891073.3950.91326430.084
BinPacker457926.262250323942037248915905140.9461972.8094.6096280.011
Shannon457926.26253069266411691552618473102604510.991877.7060.80219270.004
rnaSPAdes457926.26276473283541936775637732433068360.989910.4660.80210800.111
SPAdes 45792 6.262 44567 20542 13099 43715 40569 866 852 0.991 1089.264 0.706 570 0.088
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
Trinity928053231017162751161160321289670810.6490.595229493516625522208320.554
Trans-ABySS976557211080471451413462811649580750.6070.539354186815451506541980.495
Oases8411831206355106418317553600.2460.2023905024164101821493810.122
SOAPdenovo-Trans476222045293250550632244567825480.3760.34399412205318742713640.22
IDBA-Tran4594967531314354846967566514360.4340.391122461710514889339230.311
Bridger415721004421225346372236494223970.4670.444135621332710017302470.274
BinPacker8115198125268815548835610.8080.805192413217441000.78
Shannon203712598520671264850.2170.1958919912469441080.025
rnaSPAdes578731856064344762893269662235440.5090.48613269145539593538120.193
SPAdes 4751 2629 4919 2781 4955 2633 5155 2785 0.504 0.487 9048 9643 7028 27678 0.221



S5.2: Assembly completeness (sensitivity, true positive rate) for Mus musculus 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
Trinity0.2081.5471.983928053231017162751161160321289670811168031061120.5950.6490.9380.6390.54422949
Trans-ABySS0.2441.752.847976557211080471451413462811649580751257151111970.5390.6070.920.5970.48535418
Oases0.0241.92.8998411831206355106418317553601346486200.2020.2460.6430.2270.13239050
SOAPdenovo-Trans0.11.0311.5974762220452932505506322445678254859348519590.3430.3760.8350.3390.2589941
IDBA-Tran0.0961.0051.41245949675313143548469675665143659502520790.3910.4340.8820.40.30812246
Bridger0.0841.3481.4924157210044212253463722364942239750722457280.4440.4670.8850.4440.36113562
BinPacker0.0111.3461.409811519812526881554883561726268580.8050.8080.9630.8420.7731924
Shannon0.0041.231.5062037125985206712648510855950.1950.2170.4740.1510.0868919
rnaSPAdes0.1111.1351.45787318560643447628932696622354466016604810.4860.5090.910.4820.40713269
SPAdes0.0881.0031.2284751262949192781495526335155278552980481190.4870.5040.9060.4780.3889048



S5.3: Assembly specificity (true negative rate) for Mus musculus 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
Trinity2083235166255220.5540.940.9440.8986019510915102713
Trans-ABySS5419868154515060.4950.9380.9410.8967996093822439440
Oases14938124164101820.1220.7360.7380.697857042478587711
SOAPdenovo-Trans7136422053187420.220.8160.8140.7771930506733776916
IDBA-Tran3392317105148890.3110.8690.8680.8361810402427206090
Bridger3024713327100170.2740.7820.7850.7432117464231716680
BinPacker10013217440.780.8790.8870.8252650611788371
Shannon441089124690.0250.1430.1360.09992156841926519
rnaSPAdes538121455395930.1930.7620.7630.712362017544694169
SPAdes27678964370280.2210.7580.7580.7141655286831864625



S5.4: Various comparison and single plots for Mus musculus assemblies

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Various comparison and single plots for Mus musculus 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