Technical Help sheet

If you want to run the MGnify / MAGs Resources and Comparative Metagenomics sessions practicals in your own computers you can do so by activating the containers built for some of these sessions, and creating a Conda environment with the defined requirements for others. The Docker images are listed below, and instructions to install the conda environment are available on this link: https://github.com/EBI-Metagenomics/genome-resolved-metagenomics-2022#preparing-the-interactive-notebooks

Software requirements per session

All the software required for the practicals that took place in this course was installed on virtual machines. Here’s a complete list of the programs and applications requested by the trainers.

Software installed on Virtual Machines with Ubuntu 20.01 LTR Operating System working with
8 CPU cores ,
32 GB of RAM ,
300 GB of storage capacity,
and 8GB of GPU power ( Graphic Card )

Software list per session:

QC, and Viral annotations
Docker
Docker imagehttps://hub.docker.com/layers/microbiomeinformatics/biata-qc-assembly/v2021/images/sha256-ec91619627b5bd6704a6a88304537032acf4e2a978020b0c16e3ad981930449c?context=explore
Viral session datahttp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_courses/biata_2021/virify_tutorial.tar.gz
QC session datahttp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_courses/biata_2021/
Assembly and co-assembly
SPAdeshttps://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Linux.tar.gz
Example datahttp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_courses/ebi_2020/Assembly.tar.gz
Flyehttps://github.com/fenderglass/Flye/archive/refs/tags/2.9.1.tar.gz
megahithttps://github.com/voutcn/megahit/releases/download/v1.2.9/MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz
Bandagehttps://github.com/rrwick/Bandage/releases/download/v0.9.0/Bandage_Ubuntu-x86-64_v0.9.0_AppImage.zip
Binning and MAG generation
metaSPAdeshttps://github.com/ablab/spades/releases/tag/v3.15.3
assembly_statshttps://github.com/MikeTrizna/assembly_stats/
Bandagehttps://rrwick.github.io/Bandage/
BLASThttps://www.ncbi.nlm.nih.gov/books/NBK569861/
python3https://www.python.org/
megahithttps://github.com/voutcn/megahit
dockerhttps://docs.docker.com/get-docker/
bwahttps://sourceforge.net/projects/bio-bwa/files/
samtoolshttps://sourceforge.net/projects/samtools/files/samtools/
MetaBAThttps://bitbucket.org/berkeleylab/metabat/downloads/
CheckMhttps://github.com/Ecogenomics/CheckM
newick utilshttps://github.com/tjunier/newick_utils
FigTreehttps://github.com/rambaut/figtree
Java Runtime Environmenthttps://openjdk.org
curl, wget(implicit at the Command Line Interface)
MGnify MAG resources
Jupyter Labhttps://jupyter.org/
Minicondahttps://docs.conda.io/en/latest/miniconda.html
Python 3.8+https://www.python.org/
Githttps://git-scm.com/
Strain resoulution
STRONG https://github.com/chrisquince/STRONG
condahttps://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
Intro envhttps://raw.githubusercontent.com/Sebastien-Raguideau/strain_resolution_practical/main/conda_env_Intro.yaml
Cog databasehttps://strongtest.s3.climb.ac.uk/rpsblast_cog_db.tar.gz
Mini kraken dbhttps://genome-idx.s3.amazonaws.com/kraken/k2_standard_16gb_20220926.tar.gz
Bandagehttps://github.com/rrwick/Bandage/releases/download/v0.9.0/Bandage_Ubuntu-x86-64_v0.9.0_AppImage.zip
feh
evince
Comparative metagenome analysis
Rhttps://cloud.r-project.org/index.html