A memory-efficient algorithm to obtain splicing graphs and de novoexpression estimates from de Bruijn graphs of RNA-Seq data

Table 2 Statistics of the simulated transcriptome assemblies of Drosophila using its known complete genome over different values of k and k-mer coverage cutoff c with 0.2% mismatches in the reads. The notations are the same as in Table 1.

*k_c*	initial nodes	largest tangle	largest SCC	splicing graphs	max length	N50	>1-node graphs	max nodes	avg nodes	SNPs	total hits	unique hits	>1-hit graphs	max hits	time (mins)	memory (GB)
25_3	45305	23504	15883	13240	26909	2255	634	8671	27	2049	8258	6188	315	16	94,3	30,2
25_5	29090	16349	11411	11734	27251	2321	606	1832	11	337	8156	6180	321	12	94,3	30,2
25_10	26297	15235	10367	11606	27251	2329	595	165	8	257	8116	6176	319	13	94,3	30,2
31_3	23544	5604	2331	11993	44990	2536	583	1520	12	611	9561	8488	281	17	83,3	21,2
31_5	19869	4299	2097	11650	44990	2545	571	253	7	248	9548	8488	281	13	83,3	21,2
31_10	19541	4222	2056	11642	44990	2545	572	96	7	233	9544	8484	281	13	83,3	21,2

ISSN: 1471-2164