software
Important
You are allowed to use any software stack that you want. The following is a list of what we currently manage and where I can give you support or debugging advice. Everybody is always invited to add new options here and provide support.
The lab pipelines are currently written in Nextflow and optimized to run on a Slurm HPC cluster (optimization in progress). Thus, getting familiar with Nextflow is recommended.
We do have a lab team on https://cloud.seqera.io . If you are using Nextflow pipelines you will be added to the team for monitoring.
Current state of the lab pipelines
✓⤫ = optimized for SLURM / ✓✓ = optimized for SLURM and tested on MedBioNode
- 16S amplicon sequencing ✓✓
-
Metagenomics
- base ✓✓
- binning ✓✓
- replication rates ✓⤫
- simulation ✓✓
-
Metatranscriptomics
- with MGX ✓⤫
- de novo ✓⤫
-
Isolates/Strains
- assembly + phylogenetics ✓⤫
- replication rates ✓⤫
-
Genome-scale metabolic models
- builder ✓✓
- MEDI ✓✓
Hosting on Github as you can see 😉