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Manual for PipeCraft 2

PipeCraft is a Graphical User Interface software that implements various popular tools for metabarcoding data analyses that are linked together to generate a custom bioinformatics pipeline/workflow.

Pre-defined full pipelines for generating OTUs or ASVs are also implemented.

Panels for pipeline processes contain key options for sequence data analyses, but all options of any implemented program may be accessed via PipeCraft console (command line).

Default settings in the panels represent commonly used options for amplicon sequence data analyses, which may be tailored according to user experience or needs. Custom-designed pipeline settings can be saved, and thus the exact same pipeline may be easily re-run on other sequencing data (and for reproducibility, may be used as a supplement material in the manuscript). PipeCraft enables generation of the full pipeline (user specifies the input data and output will be e.g. OTU/ASV table with taxonomic annotations of the OTUs/ASVs), but supports also single-step mode where analyses may be performed in a step-by-step manner (e.g. perform quality filtering, then examine the output and decide whether to adjust the quality filtering options of to proceed with next step, e.g. with chimera filtering step).

Contents

• Installation
  • Prerequisites
  • Windows
  • MacOS
  • Linux
  • Updating PipeCraft2
  • Uninstalling
  • Removing Docker images
• User guide
  • The interface
  • Glossary
  • Docker images
  • Save workflow
  • Load workflow
  • Quality and basic statistics screening of the data
  • Select workdir and run analyses
  • FULL PIPELINE PANELS
  • ANALYSES PANELS
  • DEMULTIPLEX
  • REORIENT
  • CUT PRIMERS
  • QUALITY FILTERING
  • ASSEMBLE PAIRED-END reads
  • CHIMERA FILTERING
  • ITS Extractor
  • CLUSTERING
  • POSTCLUSTERING
  • ASSIGN TAXONOMY
  • POSTPROCESSING
  • Expert-mode (PipeCraft2 console)
• Walkthrough
  • Inspect quality profiles
  • Paired-end Illumina (or MGI-Tech) data
  • Single-end (PacBio or assembled paired-end) data
• Post-processing tools
  • LULU
  • DEICODE
• Troubleshooting
  • General
  • ASVs workflow
• Licence
• Contact
• How to cite
  • Work that has cited PipeCraft:
• Releases
  • 0.1.4 (15.12.2022)
  • 0.1.3 (28.07.2022)
  • 0.1.2 (07.06.2022)
  • 0.1.1 (01.04.2022)
  • 0.1.0 pre-release (14.12.2021)
• Docker images
  • Images in use
  • Other images

Manual may contain some typos! Fixing those on the way.

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Currently implemented software

See software version on the ‘Releases’ page

Software	Reference	Task
docker	https://www.docker.com	building, sharing and running applications
DADA2	Callahan et. al 2016	ASVs workflow (from raw reads to ASV table)
vsearch	Rognes et. al 2016	quality filtering, assemble paired-end reads, chimera filtering, clustering
trimmomatic	Bolger et al. 2014	quality filtering
fastp	Chen et al. 2018	quality filtering
seqkit	Shen et al. 2016	multiple sequence manipulation operations
cutadapt	Martin 2011	demultiplexing, cut primers
biopython	Cock et al. 2009	multiple sequence manipulation operations
GNU Parallel	Tangle 2021	executing jobs in parallel
mothur	Schloss et al. 2009	submodule in ITSx to make unique and deunique seqs
ITS Extractor	Bengtsson-Palme et al. 2013	extract ITS regions
fqgrep	Indraniel Das 2011	core for reorient reads
BLAST	Camacho et al. 2009	assign taxonomy
FastQC	Andrews 2019	QualityCheck module
MultiQC	Ewels et al. 2016	QualityCheck module
LULU	Frøslev et al. 2017	post-clustering curation
DEICODE	Martino et al. 2019	dissimilarity analysis

Let us know if you would like to have a specific software implemeted to PipeCraft (contacts) or create an issue in the main repository.