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Table 1 Metric trends and consistency

From: Assessing De Novo transcriptome assembly metrics for consistency and utility

Metric

Trend by

Consistent over

Trend by

Consistent over

Fully consistent

 

sequencing depth

sequencing depths

read length

read lengths

metric

Contig count

% of reads used in contigs

BP in contigs

% BP in contigs

Average contig coverage

Average unigene coverage

Contig read count COV

Unigene read count COV

Average contig length

Average unigene length

Contig N50 length

Unigene N50 length

Unique annotations in singletons

Unique annotations in contigs

Unique annotations in unigenes

Average contig OHR

Average unigene OHR

Contig RBH count

Unigene RBH count

% of Annotated contigs with RBHs

% of Annotated unigenes with RBHs

Average contig CF

Average unigene CF

Unique reverse annotations in contigs

Unique reverse annotations in unigenes

  1. Trends for de novo transcriptome assembly metrics as sequencing depth and read length are varied. Straight lines indicate monotonically increasing or decreasing trends, while curved lines indicate non-monotonic trends (either increasing then decreasing, or decreasing then increasing). Metrics are considered consistent if they consistently ranked perfectly assemblies as better; fully consistent metrics are consistent metrics with similar monotonic trends by sequencing depth and read length for perfect assemblies. Annotation-based metrics shown are computed in comparison to B. mori proteins. See Additional file 1 for full results.