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BUSCO (Benchmarking Universal Single-Copy Orthologs) — assess genome assembly, transcriptome, and proteome completeness using lineage-specific single-copy orthologs from the OrthoDB database. Reports

1 shared topic • 1 shared operation

Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem

1 shared topic • 1 shared operation

gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr

1 shared topic • 1 shared operation

MAKER — portable genome annotation pipeline that integrates ab initio gene predictors (SNAP, Augustus, GeneMark), protein and EST evidence alignment, and repeat masking to produce GFF3 gene models wit

1 shared topic • 1 shared operation

ShortBRED — metagenomics protein-family quantification tool from the bioBakery suite. Identifies short, representative peptide markers from protein families and quantifies their relative abundance in

1 shared topic • 1 shared operation