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- Hybran, a hybrid reference-based and ab initio genome annotation pipeline for prokaryotic genomes. It uses the Rapid Annotation Transfer Tool (RATT) to transfer as many annotations as possible from your reference genome annotation based on conserved synteny between the nucleotide genome sequences. Hybran then supplements unannotated regions with ab initio predictions from Prokka. Then, all coding sequence annotations are clustered together and additional reference gene names are assigned based on amino acid sequence identity and alignment coverage.
- Pbhoover, a haploid variant calling software that uses a heuristic calling algorithm in order to make base calls with high certainty in low coverage regions. This software is also capable of mixed population detection with high sensitivity.