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pharokka (version 1.3.2+galaxy0)

Bacteriophage genome:

Please upload a genome file of a bacteriophage in fasta format.

Using built-in pharokka DB:

Using built-in pharokka DB

User specified gene predictor:

Meta mode for metavirome input samples:

E-value threshold for mmseqs2 PHROGs database search. Defaults to 1E-05.:

Runs - terminase large subunit - re-orientation mode. Single genome input only and requires --terminase_strand and --terminase_start to be specified.:

Create a Zip archive of the complete output for further investigation.:

Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Pharokka identifies predicted coding sequences (CDS), transfer RNAs (tRNAs), transfer-messenger RNAs (tmRNAs) and clustered regularly interspaced short palindromic repeats (CRISPRs), providing functional annotation for CDS using the PHROGs database.

Pharokka requires assembled DNA sequences in FASTA format. For phage isolates, this usually consists of one complete contig, but Pharokka can also annotate incomplete assemblies or metavirome samples with multiple contigs in the multiFASTA format. Furthermore, metagenomically assembled phage genomes and genomic contigs, derived using programs such as Virstorter2, Hecatomb and Cenote-taker 2, are also suitable to be annotated using Pharokka using meta mode.

If you are looking for rapid standardised annotation of bacterial genomes, please use bakta.