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流程代码在：https://jihulab.com/BioQuest/SnakeMake-mNGS 或https://github.com/BioQuestX/SnakeMake-mNGS
教程链接在：https://doc.bioquest.cn/mngs

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