Markup | Genome Research

Table 1.

Summary of genome annotation methods evaluated in this study

Method	Method type	Predictions
BRAKER1	Ab initio	Protein-coding transcripts
BRAKER2	Ab initio	Protein-coding transcripts
BRAKER3	Ab initio	Protein-coding transcripts
CGP_protein	Ab initio	Protein-coding transcripts
CGP_RNA-seq	Ab initio	Protein-coding transcripts
MAKER	Ab initio	Protein-coding transcripts
StringTie + HISAT	RNA-seq assembler	Transcripts^a
StringTie + STAR	RNA-seq assembler	Transcripts^a
Scallop + HISAT2	RNA-seq assembler	Transcripts^a
Scallop + STAR	RNA-seq assembler	Transcripts^a
TOGA	Liftover	Protein-coding transcripts
Liftoff	Liftover	Protein-coding and noncoding

[i] ^aWhen paired with TransDecoder, produces CDS and UTR annotations.