Table 1.

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 0.1% mismatches in the reads.

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	38884	17900	9937	15713	37380	2366	1361	3106	10	883	12731	10162	643	27	80,3	21,2
25_5	34822	16979	9255	15521	37380	2374	1351	266	7	517	12708	10160	643	27	80,3	21,2
25_10	34494	16712	9057	15486	37380	2373	1345	194	7	481	12699	10158	639	27	80,3	21,2
31_3	28342	5037	2080	13819	45158	2704	1719	1007	7	496	12523	11112	546	12	76,3	18,2
31_5	27307	4971	1898	13740	45158	2714	1717	167	6	381	12494	11110	552	13	76,3	18,2
31_10	27265	4947	1885	13829	45158	2704	1698	161	6	377	12536	11109	542	13	76,3	18,2

Initial nodes denotes the number of nodes that are in the initial assembly. Largest tangle denotes the number of nodes of the largest connected component. Largest SCC denotes the number of nodes of the largest strongly connected component. Splicing graphs denotes the number of splicing graphs. Max length denotes the length (in nucleotides) of the longest path over all splicing graphs. N50 denotes the N50 value of the length (in nucleotides) of the longest path in each graph. >1-node graphs denotes the number of graphs with more than one node. Max nodes denotes the maximum number of nodes in these non-linear graphs. Avg nodes denotes the average number of nodes in these non-linear graphs. SNPs denotes the number of SNPs recovered. Total hits denotes the total number of hits from translated BLAST search of each node to Drosophila (isoforms are considered the same gene, only the top hit with E-value below 10⁻⁷ is included for each node in a splicing graph, and hits from nodes within the same splicing graph to the same gene are counted once). Unique hits denotes the number of unique hits to different genes. >1-hit graphs denotes the number of splicing graphs that have BLAST hits to more than one gene. Max hits denotes the maximum number of different genes that have BLAST hits to a splicing graph. Time (mins) denotes the computational time in minutes, with the values to the left and to the right of "," indicating the running time of Velvet and our postprocessing algorithm respectively. Memory (GB) denotes the memory requirement in gigabytes, with the values to the left and to the right of "," indicating the memory requirement of Velvet and our postprocessing algorithm respectively.