Table 2 Evaluation parameters used in TransFlow, described by their name, the software that calculates the parameter (FLN: Full-LengtherNext), a brief description of its meaning and the expected trend for such a parameter
Parameter name | Software | Description | Trenda |
|---|---|---|---|
AllTransSize | FLN | The sum of every transcript length in nucleotides | ↓ |
N50 | FLN | The shortest contig(or scaffold) length (in nucleotides) in the set needed to cover 50% of AllTransSize | ↑ |
N90 | FLN | The shortest contig (or scaffold) length (in nucleotides) in the set needed to cover 90% of AllTransSize | ↑ |
Contigs | FLN | Number of contigs mapping at least one pair of reads | ↓ |
Contigs500 | FLN | Same as previous, but taking into account only contigs > 500 nt | ↑ |
MeanContigLen | FLN | Mean sequence length (in nucleotides) across all useful contigs or scaffolds | ↑ |
Ns | FLN | Number of Ns (indeterminations) in the contigs or scaffolds | ↓ |
MeanGapLen | FLN | Mean indetermination length in nucleotides, where 1 indicates that gaps are randomly distributed, and greater values indicate real gaps | ↓ |
DiffProts | FLN | Number of unique, different proteins | ↑ |
DiffComplProts | FLN | Same as previous, but onlyconsidering those proteins that seem to be complete | ↑ |
MissAssembl | FLN | Percentage of contigs where the annotating protein finds similarity in both plus and minus strands | ↓ |
MeanContigCov | FLN | Fraction of the contig lengths (expressed as percentage) covered by mapped reads. This fraction is calculated per contig an then averaged for the full assembly | ↑ |
ComplOrtho | BUSCO | Percentage of OrthoDB orthologues from a lineage fully identified in one single contig | ↑ |
FragOrtho | BUSCO | Percentage of OrthoDB orthologues from a lineage that are fragmented across several contigs | ↑ |
DuplOrtho | BUSCO | Percentage of OrthoDB orthologues from a lineage that are repeated in several contigs | ↓ |