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 used in PipeCraft2 v1.2.0
Image |
Software |
Used in … |
|---|---|---|
pipecraft/vsearch_dada2:4-pc1.2.0
|
vsearch v2.30.4, DADA 1.41, (Bioconductor 3.24, R v4.6.0)
LULU v0.1.0, ORFfinder v0.4.3, seqkit v2.13.0, BLAST+
|
DADA2, UNOISE & vsearch
pipelines, chimera filtering,
clustering, SINTAX,
many QuickTools steps
|
pipecraft/funbaront:1-pc1.2.0
|
minimap2, samtools, bcftools, racon, medaka,
vsearch v2.30.4, nanoplot, chopper, filtlong,
ITSx, HMMER, BLAST, seqkit v2.13.0, nextflow,
Python 3.10.14
|
FunBarONT pipeline
|
pipecraft/nextits:1.1.0-pc1.2.0
|
NextITS v1.1.0 (extends vmikk/nextits:1.1.0),
Nextflow v25.10.4
|
NextITS pipeline
|
pipecraft/optimotu:5.1-pc1.2.0
|
optimotu_targets v5.1.0
|
OptimOTU pipeline
|
pipecraft/swarm:3.1
|
swarm v3.1.6, vsearch v2.30.4, seqkit v2.12.0,
parallel v20260122, numpy, polars
|
SWARM clustering
|
pipecraft/metamate:0.5.6-pc1.2.0
|
metaMATE v0.5.6, BBMap v39.06, seqkit v2.8.1,
mafft, R
|
metaMATE
|
pipecraft/metaworks:1.12.0-pc1.2.0
|
MetaWorks v1.12.0, ORFfinder, seqkit v2.13.0, R
|
MetaWorks (postprocessing)
|
pipecraft/blast:2.16-pc1.2.0
|
BLAST 2.16.0+, biopython, psutil v7.0.0,
seqkit v2.13.0, gawk
|
BLAST taxonomy, BlasCh
|
pipecraft/boldigger3:2.2.0
|
BOLDigger3 v2.2.0, Python 3.12
|
QuickTools: BOLDigger3
|
pipecraft/itsx:1.1.3-pc1.2.0
|
ITSx v1.1.3, ITSx_HMMs profiles 2024.04.05,
HMMER v3.4, mothur v1.46.1, seqkit v2.13.0,
biopython
|
ITSx (QuickTools and
pipelines)
|
pipecraft/cutadapt:5.2-pc1.2.0
|
cutadapt v5.2, seqkit v2.13.0, biopython
|
Cut primers
|
pipecraft/trimmomatic:0.40-pc1.2.0
|
Trimmomatic v0.40, seqkit v2.13.0
|
Quality filtering
|
pipecraft/fastp:0.23.2-pc1.2.0
|
fastp v0.23.2, seqkit v2.13.0
|
Quality filtering
|
pipecraft/reorient:1-pc1.2.0
|
fqgrep v0.4.4, seqkit v2.13.0
|
Reorient sequences
|
pipecraft/deicode:0.2.4-pc1.2.0
|
DEICODE v0.2.4, qiime2 2022.8
|
DEICODE (postprocessing)
|
ewels/multiqc:1.10 |
MultiQC v1.10 |
Quality check |
staphb/fastqc:0.11.9 |
FastQC v0.11.9 |
Quality check |
Images used in PipeCraft2 v1.1.0
Image |
Software |
Used in … |
|---|---|---|
pipecraft/vsearch_dada2:3
|
vsearch v2.29.4, dada2 v1.34,
ORFfinder v0.4.3 R v4.4.1,
seqkit v2.9.0, lulu v0.1.0
|
DADA2 pipeline,
UNOISE & vsearch pipeline,
LULU post-clustering
|
pipecraft/vsearch_dada2_m:3
|
For Mac M chips, vsearch v2.29.4, ,
dada2 v1.34, seqkit v2.9.0
lulu v0.1.0, ORFfinder v0.4.3,
R v4.4.1
|
DADA2 pipeline (Mac),
UNOISE & vsearch pipeline
LULU post-clustering (Mac)
|
ewels/multiqc:1.10 |
mutliqc v1.10 |
Quality check |
staphb/fastqc:0.11.9 |
fastqc v0.11.9 |
Quality check |
pipecraft/cutadapt:4.4
|
cutadapt v4.4, seqkit v2.3.0,
biopython v1.81, python3.10.12
|
Cut primers
|
pipecraft/reorient:1 |
fqgrep v0.4.4, seqkit v2.3.0 |
Reorient sequences |
pipecraft/trimmomatic:0.39 |
trimmomatic v0.39, seqkit v2.3.0 |
Quality filtering |
pipecraft/itsx:1.1.3
|
ITSx v1.1.3, seqkit v2.3.0,
mothur v1.46.1
|
ITSx
|
pipecraft/deicode:0.2.4 |
DEICODE v0.2.4, qiime2-2002.2 |
DEICODE |
pipecraft/fastp:0.23.2 |
fastp v0.23.2 |
Quality filtering |
pipecraft/blast:2.14
|
BLAST 2.14.0+, biopython v1.81,
gawk v5.1.0, python3.10.12
|
BLAST
|
pipecraft/metamate:1
|
metamate v0.4.0, seqkit v2.8.1,
python3.10.13, biopython v1.83
|
metaMATE
|
pipecraft/metaworks:1.12.0
|
metaworks v1.12.0, seqkit v2.3.0,
R v4.1.2, ORFfinder v0.4.3
|
|
pipecraft/optimotu:5
|
optimotu v0.9.3,
optimotu.pipeline v0.5.2,
optimotu_targets v5.0.0, R v4.3,
dada2 v1.30, cutadapt v5.0,
vsearch v2.30.0
|
OptimOTU pipeline
|
vmikk/nextits:0.5.0
|
nextITS v0.5.0,
vsearch v2.22.1,
cutadapt v4.3,
itsx v1.1.3,
blast v2.13,
seqkit v2.4.0,
fastp v0.23.2
|
NextITS pipeline
|
Images used in PipeCraft2 v1.0.0
Image |
Software |
Used in … |
|---|---|---|
pipecraft/vsearch_dada2:2
|
vsearch v2.23.0, dada2 v1.27,
ORFfinder v0.4.3 R v4.4.1,
seqkit v2.9.0, lulu v0.1.0
|
DADA2 pipeline,
UNOISE & vsearch pipeline,
LULU post-clustering
|
pipecraft/cutadapt:3.5
|
cutadapt v3.5, seqkit v2.3.0,
biopython v1.80, python3.10.6
|
Cut primers
|
ewels/multiqc:1.10 |
mutliqc v1.10 |
Quality check |
staphb/fastqc:0.11.9 |
fastqc v0.11.9 |
Quality check |
pipecraft/reorient:1 |
fqgrep v0.4.4, seqkit v2.3.0 |
Reorient sequences |
pipecraft/trimmomatic:0.39 |
trimmomatic v0.39, seqkit v2.3.0 |
Quality filtering |
pipecraft/itsx:1.1.3
|
ITSx v1.1.3, seqkit v2.3.0,
mothur v1.46.1
|
ITSx
|
pipecraft/deicode:0.2.4 |
DEICODE v0.2.4, qiime2-2002.2 |
DEICODE |
pipecraft/fastp:0.23.2 |
fastp v0.23.2 |
Quality filtering |
pipecraft/blast:2.14
|
BLAST 2.14.0+, biopython v1.81,
gawk v5.1.0, python3.10.12
|
BLAST
|
pipecraft/metaworks:1.12.0
|
metaworks v1.12.0, seqkit v2.3.0,
R v4.1.2, ORFfinder v0.4.3
|
|
vmikk/nextits:0.5.0
|
nextITS v0.5.0,
vsearch v2.22.1,
cutadapt v4.3,
itsx v1.1.3,
blast v2.13,
seqkit v2.4.0,
fastp v0.23.2
|
NextITS pipeline
|
Older images (used in PipeCraft2 vesions 0.1.X)
pipecraft/dada2:1.20
|
vsearch v2.23,
dada2 v1.20,
seqkit v2.3.0
|
pipecraft/vsearch:2.18
|
vsearch v2.18,
seqkit v2.3.0,
python3.10.6,
biopython v1.80
|
pipecraft/metaworks:1.11.2
|
metaworks v1.11.2,
seqkit v2.3.0,
R v4.1.2,
ORFfinder v0.4.3
|
pipecraft/blast:2.12
|
blast v2.12,
biopython v1.80,
gawk v5.1.0,
python3.10.6
|