A contigs has a self-chimera when a large segment of this contig is present several times in sequence. This analysis is processed with blast.
A contig is counted as included when his sequence is totally included in an other larger contig. This analysis is processed with cd-hit.
Aligns the reference proteins on contigs. Only the best hits with an identity of 80% and a coverage 80% are retained.
Uses mapping to detect when consensus has an insertion/deletion/substitution against the reads majority in this position.
Uses mapping to process by contig the percentage of R1 (single or first reads in pair) oriented in froward on the contig.
The score is designed so that an increased score is very likely to correspond to an assembly that is more biologically accurate (0 is the minimum possible score, while 1.0 is the maximum). The score is calculated as the geometric mean of all contig scores multiplied by the proportion of input reads that provide positive support for the assembly.
This score is produced by transrate (details).
Each contig is assigned a score by measuring how well it is supported by read evidence (0 is the minimum possible score, while 1.0 is the maximum.).. The contig score can be thought of as measure of whether the contig is an accurate, complete, non-redundant representation of a transcript that was present in the sequenced sample.
This score is produced by transrate (details).