Tutorials

Tutorials are available for each section listed below. To start, create a directory for the tutorial of your interest:

mkdir<section>_tutorialcd<section>_tutorial

For example, forData Preprocessing, run:

mkdirpreprocessing_tutorialcdpreprocessing_tutorial

For each of the sections we have provided a link to a conda environment file (i.e. a file that specifies which packages to install) and a test dataset that can be used for practice. Download these files and save them to the tutorial directory. Next, you can create and activate the conda environment and extract the test data:

condaenvcreate-f<environmentname>.yamlcondaactivate<environmentname>tar-xvpfSample1_isolate.tar.gz

ForGenome Assembly, you need to installmamba. Here are the commands to create the conda environment and unpack the data:

mambaenvcreate-fisolate_assembly.yamlcondaactivateisolate_assemblytar-xvpfSample1_isolate.tar.gz

Now, you are ready to run the example commands given in the corresponding section.

Data Preprocessing

Downloaddatapreprocessingcondaenvironmentfile anddatapreprocessingtestdataset

Genome Assembly

Best practices forGenome Assembly andMetagenomic Assembly.

Downloadisolateassemblycondaenvironmentfile andisolateassemblytestdataset

Taxonomic Profiling

Best practises for profiling of amplicon and metagenomic data

Transcriptomics Analysis

Best practices for transcriptomic and metatranscriptomic data analysis

Best practices in metagenomic data analysis

Support

• If you have any questions or suggestions leave a comment below!