When building a consensus the user should be able to require a certain amount of read coverage per base pair. We employ two mechanisms that can be adjust separately by the user to deal with low read coverage.
Clipping low coverage regions
Regions with a local coverage below the given threshold will be clipped from the reads before building the consensus such that the result will contain ns. This way, the user can avoid low quality tips in extensions as well as low quality regions in filled gaps. If a pile up is spanning a gap it can still be used for scaffolding if desired.
Annotating low coverage regions
Regions with a local coverage below the given threshold will be recorded in a track that marks low quality regions. This way, the user has still some idea about the sequence in these regions while maintaining knowledge about the bad quality.
When building a consensus the user should be able to require a certain amount of read coverage per base pair. We employ two mechanisms that can be adjust separately by the user to deal with low read coverage.
Clipping low coverage regions
Regions with a local coverage below the given threshold will be clipped from the reads before building the consensus such that the result will contain
ns. This way, the user can avoid low quality tips in extensions as well as low quality regions in filled gaps. If a pile up is spanning a gap it can still be used for scaffolding if desired.Annotating low coverage regions
Regions with a local coverage below the given threshold will be recorded in a track that marks low quality regions. This way, the user has still some idea about the sequence in these regions while maintaining knowledge about the bad quality.