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Table 1 Comparison of transcriptome assembled with genome-guided and genome-independent assemblers

From: Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata

  Trinity: Genome-independent assembly (GIA) Cufflinks: Genome-guided assembly (GGA)
Total length (bp) 416,036,223 301,476,740
Length with longest isoforms per locus (bp) 101,831,430 128,048,246
No. of transfrags 213,088 91,126
No. of transcripts (Unique components/gene groups) 105,664 49,971
Mean length (bp) 1,952 3,308
Longest contig (bp) 65,264 61,058
Overall mapping (%) 73.21 73.64
Concordant and unique mapping (%) 62.98 55.10
Total no. of ORFs 53,537 63,520
No. of complete ORFs 29,309 49,535
Mean length ORF (bp) 766 803
Longest ORF (bp) 63,897 54,732
Total length of assembly with CDSs only (bp) 40,889,623 48,745,723
Annotations
Against guppy (GGA against GIA or vice-versa) 40,973 (24,020) 35,147 (24,020)
Xiphophorus maculatus 19,680 (13,399) 19,941 (14,934)
Oryzias latipes 17,925 (11,102) 18,197 (12,455)
Gasterosteus aculeatus 19,139 (11,758) 19,429 (13,096)
Orthologs in only one assembly 4,767 6,954
  1. We compared a number of metrics to determine which assembler performed better. Open reading frame (ORFs) are those with a minimum length of 50 amino acids. The number of annotations obtained for each assembly are given from best Blastp hits against other protein sequence databases (E-value < 1 × 10−20). The number of orthologs (brackets) are given from reciprocal best Blastp hits identified using PROTEIN ORTHO.