Extending rnaSPAdes functionality for hybrid transcriptome assembly

BMC Bioinformatics

Table 2 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 MCF7 dataset

Assembly	Trinity	rnaSPAdes	rnaSPAdes hybrid	rnaSPAdes + Racon	rnaSPAdes + RNA-Bloom
Transcripts	305K	243K	264K	260K	270K
Misassemblies	2719	2170	3968	3001	4059
Mismatches per contig	1.85	1.50	2.31	1.82	2.26
Database coverage	0.26	0.23	0.25	0.24	0.25
Duplication ratio	2.45	1.45	2.96	2.28	2.94
50%-assembled genes	13422	13546	13990	13728	13974
95%-assembled genes	6091	6310	7379	7061	7370
50%-assembled isoforms	24575	21048	23885	22427	23795
95%-assembled isoforms	7856	7355	9333	8657	9273

Since for this dataset FL reads are available, they were fed into rnaSPAdes using the appropriate option. Best value in each row is highlighted with bold

ISSN: 1471-2105