Requirements
Requirements for running PARANOiD. Note that most requirements are fulfilled by containers and it is thus recommended to use one of the options stated in the container section. All versions shown here are fixed with PARANOiD version 1.0 and will only change with future updates to the software.
Essential
Tool |
Version |
Note |
|---|---|---|
Nextflow |
23.04.1.5866 |
Requirements when running without containers
Tool |
Version |
Note |
|---|---|---|
fastqc |
0.11.9 |
|
cutadapt |
4.2 |
|
trim_galore |
0.6.7 |
|
fastx_toolkit |
0.0.14 |
|
umi_tools |
1.1.4 |
|
python |
3.11 |
|
samtools |
1.16.1 |
|
bamtools |
2.5.2 |
|
wigToBigWig |
2.9 |
|
bigWigToBedGraph |
||
Bowtie2 |
2.5.1 |
Only when using --domain pro or running the transcript analysis |
STAR |
2.7.10b |
Only when using --domain eu |
subread |
2.0.3 |
|
pureCLIP |
1.3.1 |
Only when using peak calling |
multiqc |
1.13 |
|
pysam |
0.19.1 |
|
R |
4.0.3 |
|
optparse |
R package |
|
wig |
R package |
|
reshape2 |
R package |
|
ggplot2 |
R package |
|
numpy |
Python package |
|
biopython |
Python package |
|
gff3sort.pl |
1.0.0 |
Only when providing an annotation file |
bgzip |
1.16 |
Only when providing an annotation file |
tabix |
1.16 |
Only when providing an annotation file |
MEME |
5.4.1 |
Only when using motif detection |