Shotgun Metagenomics — Preprocessing & Host Read Removal — Hands-on

Learn how to turn raw shotgun metagenomics fastq files into clean, host-depleted readsets suitable for assembly, taxonomic and functional profiling. This module covers quality control, adapter and quality trimming, low-complexity filtering, host read removal strategies and best practices for documenting preprocessing pipelines.

Shotgun Metagenomics — Preprocessing & Host Read Removal

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Session Index

Session 1 — Raw Shotgun Reads, QC & Trimming Session 2 — Host Read Removal & Mapping Strategies Session 3 — Contaminant Depletion & Clean Readsets Session 4 — Mini Capstone: Preprocessing Pipeline Build

Session 1

Fee: Rs 8800

Raw Shotgun Reads, QC & Trimming

Shotgun read structures and metadata linkage

paired end / single end lane, run and sample IDs fastq and index files

Quality control reports and decisions

FastQC / MultiQC adapter detection overrepresented sequences

Adapter and quality trimming workflows

Trimmomatic / fastp / Cutadapt length and quality thresholds sliding window concepts

Session 2

Fee: Rs 11800

Host Read Removal & Mapping Strategies

Why host and human read removal matters

privacy and ethics coverage of microbial reads downstream sensitivity

Building host reference databases

human (GRCh) and model organisms custom host genomes index building in Bowtie2 / BWA

Mapping-based host read depletion

Bowtie2 / BWA workflows alignment parameters keeping unaligned reads

Session 3

Fee: Rs 14800

Contaminant Depletion & Clean Readsets

Integrated host and contaminant removal tools

KneadData / Sunbeam / nf-core combining trimming + mapping reference panels for contaminants

Low complexity, duplicates and quality filters

complexity filters duplicate removal options length and quality cutoffs

QC of host-depleted readsets and reporting

pre vs post read counts mapping fractions logs and MultiQC summaries

Session 4

Fee: Rs 18800

Mini Capstone: Preprocessing Pipeline Build

Designing a reproducible preprocessing pipeline

theory plus guided practical

From raw fastq to host-depleted clean reads

QC, trimming and host mapping contaminant filtering export for assembly / profiling

Deliverables and documentation checklist

pipeline script / notebook logs and QC report bundle FAIR-ready metadata for preprocessing

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Shotgun Metagenomics — Preprocessing & Host Read Removal Training | QC, Trimming & Host Depletion

Shotgun Metagenomics — Preprocessing & Host Read Removal — Hands-on