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KMAP-METAREP

KAUST Metagenomic Analysis Platform (KMAP) developed at CBRC, KAUST enables scientists to analyse (browse, query, compare) annotated metagenomic datasets. In Phase I of our re-annotation of public metagenomic datasets, we provide 4 existing and 36 newly created gene catalogs from different Earth Habitats (Project 119), providing access to over 275 million genes. Background data to KMAP are available here.
This website is free and open to all users and there is no login requirement.


To explore and analyse KMAP datasets, please access KMAP public area by clicking here or using the relevant button provided. Each of the analysis pages are provided with relevant help and filtering process. For full documentation please click on Help with Examples or watch these screencast videos.



Data in KMAP
To produce habitat specific gene catalogs, we obtained metagenomic samples from public repositories such as ENA and performed data cleaning, assembly, gene prediction (complete genes only) and gene clustering of samples from a common habitat. Representative genes from a habitat provide a habitat specific gene catalog. For annotation of gene catalogs we updated our Automatic Annotation of Microbial/MetaGenomes (AAMG) pipeline, Alam et.al, 2013 , referred here as KMAP Annotation Module. Gene Information Tables (GIT) for annotated datasets were indexed alongside hierarchical biological ontologies for taxonomic, gene ontology, enzymes, pathways, functional domains using Metagenomic Reports (MetaRep Goll et al., 2010) framework, referred to as KMAP Compare Module. See documentation for more details.



User data in KMAP

We can add annotated data sets in KMAP upon user request. For this we need Gene Information Table (GIT) formatted annotations. GIT is a simple data format, good for data exchange, data integration, data comparison and making databases, see example of GIT here, referred to as AAMG TSV.


KMAP Annotation Process module can also provide annotations in GIT format by taking user input in the form of gene catalogs (DNA or protein gene sequences from any source) or contigs from microbial genomes or metagenomes, see section on KMAP Annotation Process Module


References

1. Alam et. al., 2019. KAUST Metagenomic Analysis Platform (KMAP) enables large scale analysis of shotgun metagenomic datasets (In prep).
2. Alam et. al., 2013. INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles