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Shotgun Metagenomics: Assembly & Binning (MAGs) Training | Co-assembly, Binning, CheckM/GUNC, dRep

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Microbiome, Metagenomics & Environmental Bioinformatics >> Shotgun Metagenomics: Assembly & Binning (MAGs) Training | Co-assembly, Binning, CheckM/GUNC, dRep

Shotgun Metagenomics: Assembly & Binning (MAGs) — Hands-on

Build robust, reproducible shotgun metagenomics pipelines from raw reads to high-quality MAGs. You'll perform host/read QC, assemble (single/co-assembly) , compute coverage, bin & refine genomes, and validate MAG quality against MIMAG standards. Finish with dereplication and lightweight annotation for downstream comparative analyses.

Shotgun Metagenomics: Assembly & Binning (MAGs)
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Session 1
Fee: Rs 8800
Read QC, Host Depletion & Strategy
  • Data intake & quality control
    • FastQC / MultiQC fastp / Trimmomatic adapter/quality trimming
  • Host/contaminant read removal
    • Bowtie2 / BWA KneadData / BMTagger human/host genome filters
  • Assembly planning
    • per-sample vs co-assembly memory/CPU budgeting metadata & reproducibility
Session 2
Fee: Rs 11800
Assembly & Contig Quality
  • Assembly workflows
    • MEGAHIT / metaSPAdes SPAdes (hybrid) contig filtering (length/coverage)
  • Assembly evaluation
    • QUAST / metaQUAST N50, L50, NGA50 k-mer spectra checks
  • Gene calling for bin support
    • Prodigal / MetaGeneMark HMMs for markers
Session 3
Fee: Rs 14800
Coverage, Binning & Refinement
  • Coverage estimation
    • Bowtie2 / Minimap2 SAMtools / jgi_summarize_bam_contig_depths depth tables
  • Binning algorithms
    • MetaBAT2 / MaxBin2 / CONCOCT coverage + composition co-assembly multi-sample bins
  • Refinement & contamination checks
    • DASTool integration manual curation (Anvi'o) split/merge strategies
Session 4
Fee: Rs 18800
MAG QA/QC, Dereplication & Annotation
  • Quality assessment & standards
    • CheckM / GUNC / MIMAG tiers
  • Dereplication & redundancy control
    • dRep / ANI clustering representative MAG set
  • Lightweight annotation & export
    • Prokka / DRAM (overview) FASTA/GBK + reports ready for downstream profiling


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