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宏基因组有参分析流程

简介

此流程基于Nextflow实现。由新加坡基因组研究院(GIS)计算及系统生物学第5组(CSB5)开发。

  • 使用Nextflow最新语法，流程模块化可重复使用
  • 尽可能提供Dockerfile和Conda YAML文件，运算环境可重复
  • 提供多种环境的配置文件，GIS高性能计算(SGE)，AWS (batch)，AWS Cluster (ignite)

依赖

主流程

  • Nextflow
  • Java Runtime Environment >= 1.8

质控和去宿主DNA

  • Fastp (>=0.20.0): 去接头
  • BWA (>=0.7.17): 去宿主DNA
  • Samtools (>=1.7): 去宿主DNA

有参宏基因组分析

使用

在流程附带的数据上测试

$ shotgunmetagenomics-nf/main.nf -profile test
N E X T F L O W  ~  version 19.09.0-edge
Launching `./main.nf` [cheesy_volhard] - revision: dc7259a08e
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
executor >  local (8)
[d4/2492b7] process > DECONT (SRR1950772)  [100%] 2 of 2 ✔
[3f/d7402d] process > KRAKEN2 (SRR1950772) [100%] 2 of 2 ✔
[de/a05395] process > BRACKEN (SRR1950772) [100%] 4 of 4 ✔
Completed at: 02-Oct-2019 16:21:34
Duration    : 3m 47s
CPU hours   : 0.5
Succeeded   : 8

显示全部帮助信息

$ shotgunmetagenomics-nf/main.nf --help

N E X T F L O W  ~  version 19.09.0-edge
Launching `shotgunmetagenomics-nf/main.nf` [fabulous_feynman] - revision: e8ec2a095b
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
###############################################################################

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===============================================================================
Usage:
The typical command for running the pipeline is as follows:
  nextflow run /mnt/projects/lich/stooldrug/scratch/shotgunmetagenomics-nf/main.nf  --read_path PATH_TO_READS

Input arguments:
  --read_path               Path to a folder containing all input fastq files (this will be recursively searched for *fastq.gz/*fq.gz/*fq/*fastq files) [Default: false]
  --reads                   Glob pattern to match reads, e.g. '/path/to/reads_*{R1,R2}.fq.gz' (this is in conflict with `--read_path`) [Default: false]
  
Output arguments:
  --outdir                  Output directory [Default: ./pipeline_output/]

Decontamination arguments:
  --decont_ref_path         Path to the host reference database
  --decont_index            BWA index prefix for the host

Profiler configuration:
  --profilers               Metagenomics profilers to run [Default: kraken2,metaphlan2,humann2]

Kraken2 arguments:
  --kraken2_index           Path to the kraken2 database

MetaPhlAn2 arguments:
  --metaphlan2_ref_path     Path to the metaphlan2 database
  --metaphlan2_index        Bowtie2 index prefix for the marker genes [Default: mpa_v20_m200]
  --metaphlan2_pkl          Python pickle file for marker genes [mpa_v20_m200.pkl]

HUMAnN2 arguments:
  --humann2_nucleotide      Path to humann2 chocophlan database
  --humann2_protein         Path to humann2 protein database

AWSBatch options:
  --awsqueue                The AWSBatch JobQueue that needs to be set when running on AWSBatch
  --awsregion               The AWS Region for your AWS Batch job to run on
###############################################################################

在GIS集群上使用

$ shotgunmetagenomics-nf/main.nf -profile gis --read_path PATH_TO_READS

使用Docker容器

$ shotgunmetagenomics-nf/main.nf -profile docker --read_path PATH_TO_READS

使用AWS batch （AWS batch环境配置教程）

  • IAM配置 (在nextflow运行机器上设置环境变量AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, AWS_DEFAULT_REGION)
  • Batch 计算环境 & 作业队列
  • 定制AMI (AWS ECS optimized linux + 使用miniconda安装的awscli)
$ shotgunmetagenomics-nf/main.nf -profile test,awsbatch --awsqueue AWSBATCH_QUEUE --awsregion AWS_REGION -w S3_BUCKET --outdir S3_BUCKET

支持提供多个profile, 例如: -profile docker,test.

同时运行多个分类器

$ shotgunmetagenomics-nf/main.nf -profile gis --profilers kraken2,metaphlan2 --read_path PATH_TO_READS

应用案例

  • Chng et al. Whole metagenome profiling reveals skin microbiome dependent susceptibility to atopic dermatitis flares. Nature Microbiology (2016)
  • Nandi et al. Gut microbiome recovery after antibiotic usage is mediated by specific bacterial species. BioRxiv (2018)
  • Chng et al. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. BioRxiv (2019)

联系人

李陈浩：[email protected], [email protected]