A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms

BMC Genomics

Table 4 Transcriptome assemblies of ASplice in the blow fly C. rufifacies over different values of k and k-mer coverage cutoff c

C. ruf	splicing	max		>1-node	max	avg	D. mel	unique	>1-hit	max	mem
k_c	graphs	length	N50	graphs	nodes	nodes	hits	hits	graphs	hits	(GB)
31_50	67945	29763	1482	20900	2066	33	17516	9246	1029	15	13
31_100	52099	27855	1651	16790	2786	27	16237	9090	844	38	10
31_200	41872	35802	1717	13318	2648	21	15013	8776	624	68	9
35_50	66381	55047	1600	20465	5299	33	16470	9235	994	59	13
35_100	53120	34347	1686	16529	1398	26	15965	9062	769	14	10
35_200	41421	35802	1769	13159	4076	21	14693	8723	582	76	9

Max length denotes the length (in nucleotides) of the longest path over all splicing graphs. >1-node graphs denotes the number of splicing graphs with non-linear structures. Max nodes denotes the maximum number of nodes in a splicing graph. Avg nodes denotes the average number of nodes in splicing graphs with non-linear structures. >1-hit graphs denotes the number of splicing graphs that have BLAST hits to more than one gene in D. melanogaster. Max hits denotes the maximum number of different genes that have BLAST hits to a splicing graph. Other notations are the same as in Table 2 except that translated BLAST search to D. melanogaster is performed

ISSN: 1471-2164