Table 3.

Comparisons of the Drosophila transcriptome assemblies of our postprocessing algorithm, Oases and Trans-ABySS using six publicly available libraries over different values of k-mer coverage cutoff c.

postprocess
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)
35_3	227614	178545	88094	75367	10539	544	2048	124	6	16703	38448	10719	392	5	86,18	22,2
35_5	125414	87895	41654	47958	8678	705	1720	93	6	11334	27010	9889	429	13	86,17	22,2
35_10	57978	31785	12695	27695	6383	705	1020	63	6	5034	17271	8070	308	5	86,16	22,2
Oases
k_c	locus	max length	N50	>1-trans locus	max trans	avg trans	total hits	unique hits	>1-hit locus	max hits	time (mins)			memory (GB)
35_3	39584	15586	801	3824	13	3	29928	10898	256	4	94,28			29,32
35_5	28537	15586	936	2616	16	3	22460	10103	245	4	94,26			29,30
35_10	17075	11104	982	1377	14	3	13800	8201	185	5	94,24			29,26
Trans-ABySS
k_c	trans	max length	N50	>1-node trans	max nodes	avg nodes	total hits	unique hits	time (mins)				memory (GB)
35_3	91365	15586	898	50467	60	8	33600	10639	205,1				4,1
35_5	55164	10582	997	27763	46	7	25779	9944	195,1				4,1
35_10	28455	8865	929	13665	43	6	16032	8154	178,1				4,1

The k-mer length is fixed to 35 because Oases is only capable of assembling these libraries on machines with 32 GB physical memory when k is large. For our postprocessing algorithm, the notations are the same as in Table 1. For Oases, locus denotes the number of predicted locus, max length denotes the length of the longest predicted transcript, N50 denotes the N50 value of the longest transcript length in a predicted locus, >1-trans locus denotes the number of predicted locus with more than one transcript, max trans denotes the maximum number of transcripts in a predicted locus, avg trans denotes the average number of transcripts in predicted locus with more than one transcript, total hits denotes the total number of hits from translated BLAST search of each predicted transcript to Drosophila (isoforms are considered the same gene, only the top hit with E-value below 10⁻⁷ is considered for each transcript in a predicted locus, and hits from transcripts within the same predicted locus to the same gene are counted once), unique hits denotes the number of unique hits to different genes, >1-hit locus denotes the number of predicted locus that has BLAST hits to more than one gene, max hits denotes the maximum number of different genes that have BLAST hits to a predicted locus, 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 (without setting cov_cutoff) and Oases respectively, and 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 (without setting cov_cutoff) and Oases respectively. For Trans-ABySS, trans denotes the total number of predicted transcripts, max length denotes the length of the longest predicted transcript, N50 denotes the N50 value of the length of predicted transcripts, >1-node trans denotes the number of predicted transcripts that are the concatenation of more than one node, max nodes denotes the maximum number of nodes in a predicted transcript, avg nodes denotes the average number of nodes in predicted transcripts with more than one node, total hits denotes the total number of predicted transcripts that have BLAST hits, unique hits denotes the number of unique hits to different genes, time (mins) denotes the computational time in minutes, with the values to the left and to the right of "," indicating the running time of ABySS and Trans-ABySS respectively, and memory (GB) denotes the memory requirement in gigabytes, with the values to the left and to the right of "," indicating the memory requirement of ABySS and Trans-ABySS respectively.