Extending rnaSPAdes functionality for hybrid transcriptome assembly

BMC Bioinformatics

Table 3 Comparison between Trinity and rnaSPAdes on short-read data, and hybrid assembly performed by rnaSPAdes using raw long reads and long reads corrected with Racon and RNA-Bloom for Human siNT_48 dataset

Assembly	Trinity	rnaSPAdes	rnaSPAdes Hybrid	rnaSPAdes + Racon	rnaSPAdes + RNA-Bloom
Transcripts	463K	426K	444K	436K	443K
Misassemblies	2625	1978	2657	2389	2661
Mismatches per contig	1.78	1.32	1.43	1.39	1.43
Database coverage	0.29	0.25	0.26	0.26	0.26
Duplication ratio	2.43	1.49	2.08	1.88	2.07
50%-assembled genes	15681	15573	15570	15549	15573
95%-assembled genes	7516	7831	8186	8117	8179
50%-assembled isoforms	29150	24411	25660	24965	25669
95%-assembled isoforms	9817	9300	10038	9886	10023

ISSN: 1471-2105