bioedge/nmdc_mags repository overview

The NMDC_MAGS are wrapped around the MetaWrap⁠ pipeline for metagenome assembly and MAGs (metagenome assembled genomes) generation.

In addition to the docker image, you will need to mount some databases to /databases directory into container that you downloaded onto your host system.

⁠Download databases from web server

1. checkM database

   #CheckM database is 275MB contains the databases used for the Metagenome Binned contig quality assessment. (requires 40GB+ of memory)

    mkdir -p CHECKM_DB  && cd CHECKM_DB
    wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
    tar -xvf *.tar.gz
    rm *.gz
   

   Copy

2. NCBI taxonomy (optional for blobology and classify_bins)

   mkdir NCBI_tax && cd NCBI_tax
   wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
   tar -xvf taxdump.tar.gz
   rm *gz
   

   Copy

3. NCBI NT database (optional for blobology and classify_bins)

   mkdir NCBI_nt && cd  NCBI_nt 
   wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz"
   for a in nt.*.tar.gz; do tar xzf $a && rm $a; done
   

   Copy

⁠Usage

⁠for de novo Assembly

docker run --rm -it  -v /path/data:/data bioedge/nmdc_mags \
    metawrap assembly -t 8 -1 /data/readsX_1.fastq.gz -2  readsX_2.fastq.gz -o assembly_output --megahit

⁠for MAGs

  ## Binning
docker run --rm -it -v /path/checkM:/databases/checkM \
    -v /path/data:/data bioedge/nmdc_mags \
    metawrap binning -t 8 -a /data/assembly.fa -o bin_output --metabat2 --maxbin2 --concoct  readsX_1.fastq  readsX_2.fastq

  ## Refine Bins
docker run --rm -it -v /path/checkM:/databases/checkM \
    -v /path/data:/data bioedge/nmdc_mags \
    metawrap bin_refinement -t 8 -o refinebin_output -A /data/bin_output/metabat2_bins -B /data/bin_output/maxbin2_bins -C /data/bin_output/concoct_bins

⁠Paths to fastq and fasta data (working directory)

/data

• Note that the reads need to strictly name by xxxx_1.fastq and xxxx_2.fastq and only support paired-end reads.
• reads fastq can be gzip compressed.
• You can download example dataset from ENA. ex: SRR7877884⁠

⁠Paths to databases when mounted into the container.

/databases/checkM

/databases/NCBI_NT_DB

/databases/NCBI_TAX_DB