Zorn and Bascet can do many things:
- Preprocess reads for single-cell metagenomics, WGS and RNA-seq
- Perform de novo assembly and other tasks relevant for whole-genome sequencing
- Perform custom per-cell detailed analysis operations
The interface is designed to interoperate with Signac and Seurat for high-level analysis of the data, after the preprocessing.
Depending on your use case, you will need different tutorials. However, these are in common for all workflows:
- Installing Zorn and Bascet
- Using SLURM - If you want to run this in a high-performance environment
- Debarcoding tutorial - Ingesting raw FASTQ, trimming, and preparing for later steps
- Read-based quality control - Quality control of reads
The next step to get an overview is likely:
- KRAKEN-based workflow - if you don’t know what your sample contains, and want to compare to known species
- Alignment-based workflow - if you have some clue what your sample contains
- Informative KMER-based workflow - if you don’t know what your sample contains, and want to find novel genome compositions - Option #1
- Count sketch KMER-based workflow - if you don’t know what your sample contains, and want to find novel genome compositions - Option #2
Then there are several options on how to continue with deeper analysis:
- Clustering - to visualize your samples
- De novo assembly
- Genome annotation - annotate your assemblies
- Running software for each cell using MAP - the general method for performing calculations on each cell
These may help you understand the design of Zorn and Bascet:
- Overview of file formats
- For developers - if you wish to modify Bascet
- Example data - you can run the workflow with some small datasets before you scale up