metapi

hello, metagenomics!

• anvio
• atlas
• sunbeam

we all need a metagenomics pipeline for academic research.

• bind intelligense together
  • github
  • why we here?
• do not make wheels
  • biopython
  • bioperl
  • seqan
• make full use of pipeline execution engine
  • make
  • snakemake
  • common workflow language
  • workflow definition language
• make full use of awesome bioinformatics tools
  • bwa
  • samtools
  • spades
  • idba
  • megahit
  • metabat
  • checkm
• robust and module, extensible, update
  • one rule, one module
  • one module, one analysis
• welcome to PR

• execution module

  # Snakefile
      include: "rules/step.smk"
      include: "rules/simulation.smk"
      include: "rules/fastqc.smk"
      include: "rules/trimming.smk"
      include: "rules/rmhost.smk"
      include: "rules/assembly.smk"
      include: "rules/alignment.smk"
      include: "rules/binning.smk"
      include: "rules/cobinning.smk"
      include: "rules/checkm.smk"
      include: "rules/dereplication.smk"
      include: "rules/classification.smk"
      include: "rules/annotation.smk"
      include: "rules/profilling.smk"

• analysis module

  • raw data report
  • quality control
  • remove host sequences
  • assembly
  • assembly evaluation
  • binning
  • checkm
  • dereplication
  • bins profile
  • taxonomy classification
  • genome annotation
  • function annotation

• test module

  • execution test
  • analysis test

• install dependencies*

  • snakemake
  • pigz
  • ncbi-genome-download
  • InSilicoSeq
  • OAFilter
  • sickle
  • fastp
  • MultiQC
  • bwa
  • samtools
  • spades
  • idba
  • megahit
  • quast
  • MetaBat
  • MaxBin2
  • CheckM
  • drep
  • prokka
  • metaphlan2

  # in python3 environment
  conda install snakemake pigz ncbi-genome-download sickle-trim fastp bwa samtools \
                bbmap spades idba megahit maxbin2 prokka metabat2 drep quast checkm-genome
  pip install insilicoseq
  
  # in python2 envrionment
  conda install metaphlan2
  
  # database configuration
  wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
  mkdir checkm_data
  cd checkm_data
  tar -xzvf ../checkm_data_2015_01_16.tar.gz
  cd ..
  ln -s checkm_data checkm_data_latest
  
  # activate python3 environment where checkm in
  checkm data setRoot checkm_data_latest

• install metapi

  # recommand
  git clone https://github.com/ohmeta/metapi
  # or (maybe not latest)
  pip install metapi

• snakemake了解一下:)

  rule bwa_mem:
      input:
          r1 = "fastq/sample_1.fq.gz",
          r2 = "fastq/sample_2.fq.gz",
          ref = "ref/ref.index
      output:
          bam = "sample.sort.bam",
          stat = "sample_flagstat.txt"
      threads:
          8
      shell:
          '''
          bwa mem -t {threads} {input.ref} {input.r1} {input.r2} | \
          samtools view -@{threads} -hbS - | \
          tee >(samtools flagstat -@{threads} - > {output.stat}) | \
          samtools sort -@{threads} -o {output.bam} -
          '''

• a simulated metagenomics data test(uncomplete)

  # in metapi/example/basic_test directory
  cd example/basic_test
  
  # look
  snakemake --dag | dot -Tsvg > dat.svg

  

  # run on local
  snakemake
  
  # run on SGE cluster
  snakemake \
  --jobs 80 \
  --cluster "qsub -S /bin/bash -cwd -q {queue} -P {project} -l vf={mem},p={cores} -binding linear:{cores}"

• a real world metagenomics data process(uncomplete)

  # in metapipe directory
  # look
  cd metapi
  snakemake --dag | dot -Tsvg > ../docs/dat.svg

  

  # run on local
  snakemake \
  --cores 8 \
  --snakefile metapi/Snakefile \
  --configfile metapi/metaconfig.yaml \
  --until all
  
  # run on SGE cluster
  snakemake \
  --snakefile metapi/Snakefile \
  --configfile metapi/metaconfig.yaml \
  --cluster-config metapi/metacluster.yaml \
  --jobs 80 \
  --cluster "qsub -S /bin/bash -cwd -q {cluster.queue} -P {cluster.project} -l vf={cluster.mem},p={cluster.cores} -binding linear:{cluster.cores} -o {cluster.output} -e {cluster.error}"
  --latency-wait 360 \
  --until all

• init

  metapi --help
  
  usage: metapi [subcommand] [options]
  
  metapi, a metagenomics data process pipeline
  
  optional arguments:
      -h, --help     show this help message and exit
      -v, --version  print software version and exit
  
  available subcommands:
  
      init         a metagenomics project initialization
      simulation   a simulation on metagenomics data
      workflow     a workflow on real metagenomics data

  please supply samples.tsv
  format

  id	fq1	fq2
  s1	s1.1.fq.gz	s1.2.fq.gz
  s2	s2.1.fq.gz	s2.2.fq.gz

  python /path/to/metapi/metapi/metapi.py init -d . -s samples.tsv -b raw -a metaspades

• list

  snakemake --snakefile /path/to/metapi/metapi/Snakefile --configfile metaconfig.yaml --list

• debug

  snakemake --snakefile /path/to/metapi/metapi/Snakefile \
      --configfile metaconfig.yaml \
      -p -r -n --debug-dag \
      --until checkm_lineage_wf

• simulation

• workflow