Docker images 
Docker images (with the bioinformatic tools) used in PipeCraft2 are stored on Dockerhub. These images can be used to launch any tool with the Docker CLI to utilize the compiled tools.
Images in use
Image |
Software |
|---|---|
pipecraft/vsearch_dada2:2 |
vsearch v2.23, dada2 v1.27, seqkit v2.3.0, lulu v0.1.0, R, GNU parallel etc |
ewels/multiqc:latest |
mutliqc v1.12 |
staphb/fastqc:0.11.9 |
fastqc v0.11.9 |
pipecraft/cutadapt:3.5 |
cutadapt v3.5, seqkit v2.3.0, python3, biopython |
pipecraft/reorient:1 |
fqgrep v0.4.4, seqkit v2.3.0 |
pipecraft/trimmomatic:0.39 |
trimmomatic 0.39, seqkit v2.3.0 |
pipecraft/itsx:1.1.3 |
ITSx v1.1.3, seqkit v2.3.0, mothur v1.46.1 |
pipecraft/deicode:0.2.4 |
DEICODE v0.2.4, qiime2-2002.2 |
pipecraft/fastp:0.23.2 |
fastp v0.23.2 |
pipecraft/blast:2.12 |
BLAST 2.12.0+, biopython, python3, gawk |
Other images
Image |
Software |
|---|---|
pipecraft/dada2:1.20 |
dada2 v1.20, seqkit v2.3.0, lulu v0.1.0, R |
pipecraft/vsearch:2.18 |
vsearch v2.18, seqkit v2.3.0, GNU parallel |
pipecraft/vsearch_dada2:1 |
has issues with MacOS. vsearch v2.22.1, dada2 v1.20, seqkit v2.3.0, lulu v0.1.0, R, GNU parallel |