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Brucellosis Incidence
Brucella Prevalence
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Prokka
Prokaryotic genome annotation
snippy
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads
ABRicate
Mass screening of contigs for antimicrobial and virulence genes
FASTTREE
build maximum-likelihood phylogenetic trees
Shovill
Assemble bacterial isolate genomes from Illumina paired-end reads
Prokka
Use Test Data and Preset Parameters
Contigs to annotate
Upload a query fasta file. (Required)
upload
FASTA format
Locus tag prefix (--locustag)
Locus tag counter increment (--increment)
1
GFF version (--gffver)
3
2
1
Force GenBank/ENA/DDJB compliance (--compliant)
Yes
No
Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below)
Add 'gene' features for each 'CDS' feature (--addgenes)
Yes
No
Minimum contig size (--mincontiglen)
NCBI needs 200
200
Sequencing centre ID (--centre)
Genus name (--genus)
May be used to aid annotation, see --usegenus below
Species name (--species)
Strain name (--strain)
Plasmid name or identifier (--plasmid)
Kingdom (--kingdom)
Archaea
Bacteria
Mitochondria
Viruses
Use genus-specific BLAST database (--usegenus)
Yes
No
Optional FASTA file of trusted proteins to first annotate from (--proteins)
Upload a optional reference fasta file.
upload
Citation(s)
Seemann T.
Prokka: rapid prokaryotic genome annotation
Bioinformatics
2014 Jul 15;30(14):2068-9.
PMID:24642063