Long Read Metagenomics ONT & PacBio — Hands-on

Learn how to design and execute long read metagenomics projects using Oxford Nanopore Technologies (ONT) and PacBio platforms. This module covers platform concepts, QC and basecalling, long read mapping and assembly, polishing strategies and structural variant aware analysis for complex microbial communities.

Long Read Metagenomics ONT & PacBio

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Session Index

Session 1 — Long Read Metagenomics Foundations & Platforms Session 2 — ONT & PacBio QC, Basecalling & Alignment Session 3 — Long Read Assembly, Polishing & SV Analysis Session 4 — Mini Capstone: Long Read Metagenome Pipeline

Session 1

Fee: Rs 8800

Long Read Metagenomics Foundations & Platforms

Why long reads for metagenomics

contiguity and resolving repeats plasmids, phages and mobile elements haplotypes and structural variation

ONT & PacBio platform basics

flow cells, chemistries and run parameters read length, yield and error profiles HiFi vs noisy long reads

Sample and library design for long read metagenomes

high molecular weight DNA requirements host depletion and complexity considerations designing runs and multiplexing strategies

Session 2

Fee: Rs 11800

ONT & PacBio QC, Basecalling & Alignment

Raw data handling and basecalling concepts

signal level data and basecalling workflows quality scores and filtering thresholds demultiplexing barcoded libraries

QC for long read metagenomic datasets

read length and quality distributions adapter trimming and chimeric reads host read screening and removal

Mapping long reads for metagenomic contexts

long read aligners and options coverage, identity and error diagnostics exporting BAM and summary statistics

Session 3

Fee: Rs 14800

Long Read Assembly, Polishing & SV Analysis

Assembly of long read metagenomes

long read assemblers for complex communities contig evaluation and fragmentation patterns circular contigs and plasmids

Polishing strategies and error correction

long read only polishing passes short read assisted polishing concepts tracking improvements with quality metrics

Structural variation and genomic architecture glimpses

detecting large insertions and deletions rearrangements in MAGs and contigs visualising alignments and breakpoints

Session 4

Fee: Rs 18800

Mini Capstone: Long Read Metagenome Pipeline

End to end long read metagenomics workflow

theory plus guided practical

From raw ONT or PacBio reads to polished assemblies

QC, basecalling and filtering assembly and polishing steps chained simple annotation ready outputs

Deliverables: pipeline scripts, QC summary and report

command log or workflow file QC and assembly metrics tables PDF or HTML long read metagenome report

PDF

Long Read Metagenomics ONT & PacBio Training | Long Read Workflows for Microbial Communities

Long Read Metagenomics ONT & PacBio — Hands-on