etheleon/metamapsdb repository overview

⁠MetamapsDB

.

MetamapsDB is a R package used for interfacing with such a database for Gene centric queries and Analyses of Integrated Genomic and Transcriptomic microbiome data. It is the final step of the 5 preprocessing steps used in carrying out our gene centric pipeline. (Unpublished)

Annotation DIAMOND - Labelling of short reads using, blastX-like against NR protein database (more for functional) Binning MEGAN6 CE - Functional (KEGG) binning of NGS short reads based on labels Bin-based Assembly NEWBLER - Gene Centric OLC Assembly of functional bins / KEGG Orthologs Gene centric analyses pAss - mapBlat - Maps (using BLAT) gDNA and rRNA short onto

⁠Bin-Based assembly

• Annotation DIAMOND - Labelling (round2) more for taxonomic annotation
• MEGAN6 CE - Taxonomic binning of contigs based on labels

⁠Gene centric Analysis

• Identify Maximum Diversity Region (MDR)
• Remove known KOs which fail process
  • Diversity analysis (gene count)
    • 31 Single Copy Genes
  • ID genera which are indistinguishable due to sequence conservation

⁠mapBlat

• the contigs
• just the MDR Region

⁠Dependencies

⁠R Bioconductor packages

If you're installing this package from from a conda installation of R, it's very likely you'll face some issues with installing ShortRead.

conda install -c bioconda -c conda-forge bioconductor-shortread

⁠OMICS

Graph based database⁠ combining KEGG + Taxnoomy + Sequencing data (contig) .

⁠MapBlat

R package for mapping reads onto contigs/MDR using Blat

mapBlat⁠

⁠Functions

Below is a description of important functions and their uses