mNGS Pipeline summary

Metagenomic next-generation sequencing

Reference

Genome refence was download from Ensembl

Alignment

1. Adapter trimming (fastp)
2. Aligner (BWA mem2)
3. Mark duplicates (samblaster)
4. Merge CRAMs of every sample, repesectly (Picard)
5. Create CRAM index (samtools)

Quality control report

1. Fastp report (MultiQC)
2. Alignment report (MultiQC)

Taxonomic classification

1. Taxonomic classification using exact k-mer matches (Kraken)
2. Classifier for metagenomic sequences (Centrifuge)
3. Computes the abundance of species in DNA sequences (Bracken)
4. Krona plot (Krona)

Assemble

1. Metagenome assemblier (Spades)
2. Resistance Gene Identifier (RGI)
3. Virulence factor predication (diamond)

SnakeMake Report

Outputs

.
├── config
│   ├── config.yaml
│   └── samples.tsv
├── dag.svg
├── logs
│   ├── align
│   ├── bracken
│   ├── centrifuge
│   ├── fastp
│   ├── kraken2
│   ├── kreport2krona
│   ├── Krona
│   ├── MergeSamFiles
│   ├── qc
│   ├── RemoveHost
│   ├── rgi
│   ├── spades
│   └── VFDB
├── raw
│   ├── SRR10903401.1.fastq.gz
│   ├── SRR10903401.2.fastq.gz
│   ├── SRR10903402.1.fastq.gz
│   └── SRR10903402.2.fastq.gz
├── README.md
├── report
│   ├── align_multiqc_data
│   ├── align_multiqc.html
│   ├── bracken
│   ├── centrifuge
│   ├── fastp_multiqc_data
│   ├── fastp_multiqc.html
│   ├── kraken2
│   └── Krona
├── report.html
├── results
│   ├── aligned
│   ├── centrifuge
│   ├── kraken2
│   ├── kreport2krona
│   ├── rgi
│   ├── spades
│   └── VFDB
└── workflow
    ├── envs
    ├── report
    ├── rules
    ├── schemas
    ├── scripts
    └── Snakefile

Directed Acyclic Graph

Krona Plot