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REQUIREMENTS.rst

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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 <section-container>. 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 <domain> or running the transcript analysis <transcript-analysis>
STAR 2.7.10b Only when using --domain eu <domain>
subread 2.0.3
pureCLIP 1.3.1 Only when using peak calling <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 <annotation>
bgzip 1.16 Only when providing an annotation file <annotation>
tabix 1.16 Only when providing an annotation file <annotation>
meme 5.4.1 Only when using motif detection <motif-detection>