Requirements
Requirements to run PARANOiD. Note that most are fulfilled by containers and it's thus recommended to use one of the options stated in the container section. All versions shown here ae fixed with PARANOiD version 1.0 and will only change with future updates.
Essential
Tool |
Version |
Note |
|---|---|---|
Nextflow |
23.04.1.5866 |
Requirements when run without container
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 |