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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.