BMC Bioinformatics

Table 1 Transcriptome sequencing and assembly summary

From: Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

	k-19	k-21	k-23	k-27	k-33	k-37	k-43	k-53	k-63
Sequencing
Raw sequencing reads					44,568,122
Read length					99
Pre-assembly
Reads requiring trimming					29,264,547
Minimum read length					1
Lower quartile read length					65
Median read length					87
Upper quartile read length					99
Maximum read length					99
Assembly
Number of reads assembled	18,097,635	18,481,043	18,018,855	16,878,820	16,918,312	17,188,419	26,970,166	30,231,540	28,058,816
Number of reads mapped	28,449,200	31,893,197	33,199,219	32,903,930	33,395,304	32,523,018	31,939,290	30,267,756	27,808,027
Number of contigs (≥ 100 bp)	98,094	64,000	47,448	46,461	40,965	46,442	34,489	33,344	32,639
Number of contigs (≥ 5,000 bp)	470	1,296	1,587	1, 315	1,025	742	636	253	115
Number of contigs (≥ 8,000 bp)	42	155	215	165	119	72	105	17	22
Average length of contigs	700	1,114	1,463	1,356	1,383	1,115	1,402	1,120	914
Longest contig length	46,754	29,394	16,393	14,115	13,754	13,685	12,571	9,484	12,582
N50	1,594	2,415	2,745	2,624	2,497	2,202	2,349	1,836	1,498
N90	249	470	795	696	733	488	730	515	372

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ISSN: 1471-2105

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