System requirements
System
Nadiatools requires a linux system. It is extensively tested on Ubuntu.
STARsolo pipeline requires more RAM and computational power than Alevin-fry pipeline. It is recommended to have at least 8-core CPUs and 32GB of RAM. The disk space depends on the amount of data (500GB recommended).
Dependencies
Nadiatools require following softwares to be installed:
Softwares |
Version |
|---|---|
fastqc |
0.11.9 |
cutadapt |
4.1 |
star |
2.7.10a |
salmon |
1.9.0 |
alevin-fry |
0.8.0 |
AlevinQC |
1.14.0 |
multiqc |
1.13 |
anndata |
0.8.0 |
scanpy |
1.9.1 |
scipy |
1.9.3 |
harmonypy |
0.0.6 |
scanorama |
1.7.3 |
scrublet |
0.2.3 |
umap-learn |
0.5.3 |
matplotlib |
3.6.1 |
numpy |
1.23.4 |
pandas |
1.5.1 |
plotly |
5.11.0 |
seaborn |
0.11.2 |
biopython |
1.79 |
sphinx |
5.3.0 |
sphinx-rtd-theme |
1.1.1 |
python |
3.7 |
R |
4.2.2 |