De novo transcriptome assembly: A comprehensive cross-species comparison of
short-read RNA-Seq assemblers

Supplementary Data

Martin Hölzer and Manja Marz

Back to main supplement page

RNA-Quast contents for Arabidopsis thaliana

• S5.1: Short report for Arabidopsis thaliana assemblies
• S5.2: Assembly completeness (sensitivity, true positive rate) for Arabidopsis thaliana assemblies
• S5.3: Assembly specificity (true negative rate) for Arabidopsis thaliana assemblies
• S5.4: Various comparison and single plots for Arabidopsis thaliana assemblies

S5.1: Short report for Arabidopsis thaliana assemblies

METRICS/TRANSCRIPTS	Genes	Avg. number of exons per isoform	Transcripts	Transcripts > 500 bp	Transcripts > 1000 bp	Aligned	Uniquely aligned	Multiply aligned	Unaligned	Avg. aligned fraction	Avg. alignment length	Avg. mismatches per transcript	Misassemblies	Database coverage
Trinity	32833	5.813	34617	21969	13357	34432	32388	44	185	0.993	978.213	1.315	1212	0.298
Trans-ABySS	32833	5.813	66004	31763	19714	65463	56460	176	541	0.979	745.088	0.612	7227	0.334
Oases	32833	5.813	57809	47279	32647	57441	48302	66	368	0.988	1232.688	3.471	6804	0.321
SOAPdenovo-Trans	32833	5.813	50876	17326	8709	50525	50289	119	351	0.997	561.746	0.099	51	0.299
IDBA-Tran	32833	5.813	32447	18147	9577	32366	32020	54	81	0.998	848.356	0.136	201	0.289
Bridger	32833	5.813	30017	20235	12882	29822	25907	45	195	0.99	990.349	2.427	1995	0.256
BinPacker	32833	5.813	5914	5458	3775	5891	3945	8	23	0.976	1312.171	5.902	1233	0.047
Shannon	32833	5.813	27685	18623	12018	27478	25912	37	207	0.996	1044.904	0.724	769	0.245
rnaSPAdes	32833	5.813	36953	18068	11160	36628	35821	91	325	0.995	807.422	0.341	505	0.3
SPAdes	32833	5.813	29929	17390	11171	29691	27985	62	238	0.993	944.388	0.43	1189	0.279

METRICS/TRANSCRIPTS	50%-assembled genes	95%-assembled genes	50%-covered genes	95%-covered genes	50%-assembled isoforms	95%-assembled isoforms	50%-covered isoforms	95%-covered isoforms	Mean isoform coverage	Mean isoform assembly	50%-matched	95%-matched	Unannotated	Mean fraction of transcript matched
Trinity	12459	2196	14388	2542	13304	2302	15266	2651	0.684	0.625	30436	26763	887	0.92
Trans-ABySS	13755	1881	15660	2200	15283	1960	17334	2298	0.639	0.582	50342	41811	3066	0.866
Oases	13955	2599	14680	2812	15861	2753	16686	2981	0.734	0.707	46508	39238	788	0.933
SOAPdenovo-Trans	11457	1213	15357	1770	11470	1213	15395	1770	0.591	0.489	44555	42150	2479	0.887
IDBA-Tran	12672	1175	14963	1642	12694	1175	15017	1642	0.654	0.579	30039	28142	801	0.929
Bridger	11301	1861	12519	2076	11814	1909	13047	2127	0.666	0.623	24213	21017	876	0.911
BinPacker	2589	477	2609	488	2706	489	2729	500	0.751	0.745	3808	2929	23	0.917
Shannon	11168	1962	12207	2103	11606	2004	12658	2147	0.698	0.657	24594	22274	854	0.929
rnaSPAdes	12931	2233	15136	2607	13051	2237	15283	2613	0.672	0.603	32784	28995	1938	0.896
SPAdes	12496	2318	13998	2570	12509	2318	14031	2570	0.681	0.632	25910	22414	1100	0.902

S5.2: Assembly completeness (sensitivity, true positive rate) for Arabidopsis thaliana assemblies

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/TRANSCRIPTS	Database coverage	Duplication ratio	Avg. number of transcripts mapped to one isoform	50%-assembled genes	95%-assembled genes	50%-covered genes	95%-covered genes	50%-assembled isoforms	95%-assembled isoforms	50%-covered isoforms	95%-covered isoforms	50%-assembled exons	95%-assembled exons	Mean isoform assembly	Mean isoform coverage	Mean exon coverage	Avg. percentage of isoform 50%-covered exons	Avg. percentage of isoform 95%-covered exons
Trinity	0.298	1.128	1.517	12459	2196	14388	2542	13304	2302	15266	2651	91985	66950	0.625	0.684	0.893	0.736	0.42
Trans-ABySS	0.334	1.341	2.142	13755	1881	15660	2200	15283	1960	17334	2298	99841	71380	0.582	0.639	0.868	0.686	0.377
Oases	0.321	1.976	2.318	13955	2599	14680	2812	15861	2753	16686	2981	96063	71517	0.707	0.734	0.904	0.795	0.477
SOAPdenovo-Trans	0.299	1.008	1.963	11457	1213	15357	1770	11470	1213	15395	1770	94715	65284	0.489	0.591	0.858	0.63	0.329
IDBA-Tran	0.289	1.01	1.481	12672	1175	14963	1642	12694	1175	15017	1642	94428	68543	0.579	0.654	0.89	0.707	0.384
Bridger	0.256	1.067	1.372	11301	1861	12519	2076	11814	1909	13047	2127	81178	59493	0.623	0.666	0.887	0.715	0.407
BinPacker	0.047	1.149	1.203	2589	477	2609	488	2706	489	2729	500	15632	11737	0.745	0.751	0.911	0.818	0.489
Shannon	0.245	1.185	1.499	11168	1962	12207	2103	11606	2004	12658	2147	77697	57086	0.657	0.698	0.894	0.755	0.427
rnaSPAdes	0.3	1.027	1.608	12931	2233	15136	2607	13051	2237	15283	2613	95185	69477	0.603	0.672	0.889	0.721	0.404
SPAdes	0.279	1.007	1.406	12496	2318	13998	2570	12509	2318	14031	2570	89800	66775	0.632	0.681	0.895	0.733	0.419

S5.3: Assembly specificity (true negative rate) for Arabidopsis thaliana assemblies

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/TRANSCRIPTS	Unannotated	50%-matched	95%-matched	Mean fraction of transcript matched	Mean fraction of block matched	50%-matched blocks	95%-matched blocks	Matched length	Unmatched length
Trinity	887	30436	26763	0.92	0.961	0.963	0.94	30013045	1997896
Trans-ABySS	3066	50342	41811	0.866	0.96	0.961	0.938	39985550	2854902
Oases	788	46508	39238	0.933	0.956	0.959	0.937	56614558	3847059
SOAPdenovo-Trans	2479	44555	42150	0.887	0.966	0.963	0.95	26902613	1538113
IDBA-Tran	801	30039	28142	0.929	0.975	0.976	0.96	26093803	1200078
Bridger	876	24213	21017	0.911	0.962	0.964	0.943	24386684	1678489
BinPacker	23	3808	2929	0.917	0.942	0.945	0.918	4857682	495914
Shannon	854	24594	22274	0.929	0.971	0.973	0.955	25918151	1383207
rnaSPAdes	1938	32784	28995	0.896	0.968	0.972	0.944	27457743	1771614
SPAdes	1100	25910	22414	0.902	0.965	0.969	0.94	25038690	1699469

S5.4: Various comparison and single plots for Arabidopsis thaliana assemblies

Various comparison and single plots for Arabidopsis thaliana assemblies. For detailed descriptions of each plot please check the RNA-Quast manual page:

alignment_multiplicity	mismatch_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_exons	blocks_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
NAx	x-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_length	x-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-matched	transcript_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
Nx	x-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-assembled	x-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