Genome quality & annotation

Metagenomics Tools

Genome download

→ NCBI refseq and genbank

Genome quality control

→ CheckM

to estimate genome com­pleteness and contamination based on common single-​copy genes

Genome annotation

→ Prokka

Annotation tool for bacterial, archaeal, and viral genomes

→ RAST server

for bacterial and archaeal genomes

→ Maker

eukaryotic and prokaryotic genomes

→ GeneMark

- eukaryotics; prokaryotics; viruses, pages and plasmids

- part of genome annotation pipelines at NCBI

→ MetaGeneMark

gene identification in metagenomic sequences

Pathway / gene / protein databases


gene annotation and pathway database

→ KEGG KAAS server

multiple sequence annotation

→ WikiPathways

Community edited pathway database

→ UniProt

Gene annotation and protein database

→ Pfam

Gene annotation and protein database

Converting gene/protein/pathways identifiers

convert UniProt, KEGG, EMBL, RefSeq, ... identifiers

UniProf or NCBI-geneIDs to KEGG