Metagenome Annotation Pipeline

Analysis summary

Analysis statistics: master.stats.txt

Analysis annotation in gff format: master.gff.txt

Analysis annotation in tbl format: master.tbl.txt

Analysis annotation in tab delimited format: master.tsv.txt

Ab initio gene prediction & annotation

MetaErg begins biological feature and element prediction by identifying CRISPR elements and non-coding RNA genes (tRNA, rRNA genes). Next, to avoid identification of artefactual protein coding genes overlapping with detected non-coding features, MetaErg masks these features by replacing them with Ns. Metagenome function annotation is very similar to genomic annotation and relies on comparisons of predicted genes with existing, previously annotated sequences.

Gene Type Genecalling Tools Annotation Tools Browse Genes
CRISPR minced N/A Tabular txt view
Interactive table view
Sequence file: crispr.ffn
tRNA aragorn N/A Tabular txt view
Interactive table view
Sequence file: tRNA.ffn
All rRNA rRNAFinder.pl Blastn Tabular txt view
Interactive table view
-- 16SrRNA Blastn search against SILVA SSU 132 Sequence file: 16SrRNA.ffn
-- 18SrRNA Blastn search against SILVA SSU 132 Sequence file: 18SrRNA.ffn
-- 23SrRNA Blastn search against SILVA LSU 132 Sequence file: 23SrRNA.ffn
-- 28SrRNA Blastn search against SILVA LSU 132 Sequence file: 28SrRNA.ffn
-- 5SrRNA Blastn Sequence file: 5SrRNA.ffn
All CDs Prodigal_v2.6.1 Diamond
Hmmearch		 Sequence files: cds.ffn ,and cds.faa
-- Swiss-Prot annotations Diamond Tabular txt view
-- Pfam annotations Hmmearch Tabular txt view
-- Tigrfam annotations Hmmearch Tabular txt view
-- Casgene annotations Hmmearch Tabular txt view
-- Metabolic annotations Hmmearch Tabular txt view
-- Genomedb annotations Diamond Tabular txt view
-- EC annotations Inferred from FOAM, Swiss-Prot, and Tigrfam annotations Tabular txt view
gene2ec mapping txt
-- KO annotations Inferred from FOAM, and Swiss-Prot annotations Tabular txt view
gene2ko mapping txt
-- GO annotations Inferred from Pfam, and Swiss-Prot annotations Tabular txt view
-- KEGG annotations MinPath program using gene2ko mapping file as input Tabular txt view
-- MetaCyc annotations MinPath program using gene2ec mapping file as input Tabular txt view

Notes: cds.gene2ko.mapping.txt file can be used as an input to KEGG Mapper to reconstruct, search, and color pathways

Taxonomic profiles based on different genes

MetaErg classifies all ORFs based on the best Diamond search hit against a custom database, GenomeDB. All the rRNA genes were classified based on the best Blastn search hit against SILVA SSU and LSU databases.

Gene Type Browsing taxonomic profiles & interactive visualization
SSU rRNA Tabular profile, and interactive table, tree, gene count sunburst, gene abundance sunburst views
LSU rRNA Tabular profile, and interactive table, tree, gene count sunburst, gene abundance sunburst views
CDs Tabular profile, and interactive table, tree, gene count sunburst, gene abundance sunburstviews

Function profiles

Database Profiles and visualizations
Pfam Tabular profile, and interactive table view
Tigrfam Tabular profile, and interactive table view
Metabolic-hmm
(Metaboic marker gene for specific pathways) 		Tabular profile, and interactive table, tree, gene count sunburst, gene abundance sunburst views
KO (KEGG Orthology) Tabular profile, and interactive table view
Enzyme Tabular profile, and interactive table view
GO (Gene Ontology) Tabular profile, and interactive table view

Pathway profiles

MetaErg constructs pathways using MinPath to get the conservative estimate of the pathways present in an analysis. MinPath only considers the minimum number of pathways required to explain the set of enzymes in the analysis instead of attempting to reconstruct entire pathways from a given set of enzymes identified in the analysis.

Pathways Summaries and interactive visualization
KEGG pathways Tabular profile, and interactive table view
MetaCyc pathways Tabular profile, and interactive table view