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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