Releases 

1.1.0 (12.03.2025)

added Resource Manager to control the resources used by Docker containers
added OptimOTU pipeline for Fungi and Metazoa
added metaMATE tool for filtering COI reads
added SINTAX classifier
added sim_score (pident * (alignment length / qlen) and adj_qcov (if qlen > slen then ((send-sstart+1)/slen)*100, otherwise equal to qcovs) to BLAST results
sequences are now also added to the OTU table
added support to process and merge multiple sequencing runs (runs must be in multiRunDir directory)
tag-jumps filtering module (UNCROSS2) in now in the pre-defined pipelines (curate table box)
NextITS in now available in MacOS
removed read_R1 string input requirement (PE files must contain R1 and R2, then the PE samples will be automatically detected)
removed HMM search from ORFfinder (now only ORFfinder is available); HMM did not work properly.
added RAM friendly DADA2 pipeline implementation for denoising (“dada2 Big Data”)
added fix to CUT PRIMERS module to properly clip primers when PE amplicons are shorter than the sequencing cycle
added fix to UNOISE pipeline to remove chimeras also from the table, not oonly form the final fasta file
disabled automatic clustering in UNOISE pipeline; zOTUs can be clustered with ASV TO OTU module
added min_lenght option back to demultiplexing module
updated and fixed multiQC module to merge fastqc reports

Implemented software: (software in red font denote new additions; ‘version’ in bold denotes version upgrade)

Software	version
OptimOTU https://github.com/brendanf/optimotu_targets	5.1.0
SINTAX (via vsearch)	2.29.4
metaMATE https://github.com/tjcreedy/metamate	0.4.3
NextITS pipeline	0.5.0
ORFfinder	v0.4.3
RDP classifier	v2.13
DADA2	1.34
vsearch	2.29.4
trimmomatic	0.39
seqkit	2.3.0
cutadapt	4.4
mothur	1.46.1
ITS Extractor	1.1.3
fqgrep	0.4.4
BLAST	2.14.0+
FastQC	0.11.9
MultiQC	1.12
LULU	0.1.0
fastp	0.23.2
DEICODE	0.2.4

major updates in the front-end; individual tools on the right, pipelines on left.
added debugging mode and improved log info
added NextITS pipeline for PacBio ITS sequences (not available for MacOS release)
added ORFfinder + HMM bsed pseudogene/off-targets filtering for protein coding genes
added RDP classifier
added DADA2 pipeline for PacBio data
added DADA2 pipeline for paired-end mixed oriented amplicons (fwd_orient and rev_orient are denoised separately and then merged)
implemented DADA2 denoising sensitivity editing
all features will get sha1 ID
added ASVs to OTUs module (cluster ASVs into OTUs with vsearch)
added tag-jumps filtering module (UNCROSS2)
fixed the vsearch_dada2 container issues for MacOS

Implemented software: (software in red font denote new additions; ‘version’ in bold denotes version upgrade)

added 2nd round of cut primers to properly remove fwd and rev primers form the paired-end data set
added UNOISE3 module to generate zOTUs (under clustering)
added uchime3 chimera filtering (for denoised amplicons)
edited sequence count statistics process after the process (using seqkit)
only fasta (fa, fas) format is accepted for clustering
edited OTU table making strategy for OTU clustering (was –usearch_global before)
added table filtering options for DADA2 ASV table (collapse mismatch, filter by length)
added ASV to OTU module (clustering DADA2 ASVs into OTUs)
select region to cluster after ITSx in OTUs workflow
automatically saves the PipeCraft workflow settings into loadable JSON file
outputs log file (in development)
merged vsearch and dada2 containers (had a lot in common)

Implemented software: (software version in bold denotes version upgrade)

updated BLAST 2.11.0+ to BLAST 2.12.0+ and added biopython to BLAST container (fixed the coverage% calculation)
fixed the megaBLAST, when gapextend=undefined
quality Check module edit (does not stop when browsing around)
fixed ASVs workflow error message when using <2 samples
added lock panels when starting a process
few cosmetic front-end adds

added LULU post-clustering
added DEICODE (postprocessing)
added fastp quality filtering
added DADA2 quality filtering under ‘ADD STEP’ -> ‘QUALITY FILTERING’ panel
added DADA2 denoise and assemble paired-end data under ‘ADD STEP’ -> ‘ASSEMBLE PAIRED-END’ panel
added DADA2 assignTaxonomy under ‘ADD STEP’ -> ‘ASSIGN TAXONOMY’ panel
added trunc_length option for vsearch quality filtering
python3 module fix for ITSx for removing empty sequeces

Implemented software: (software in red font denote new additions; ‘version’ in bold denotes version upgrade)

Minor cosmetic changes and bug fixes. DOWNLOAD link for v0.1.1

separate output forlder for unused index combinations in demultiplexing.
resolved issues with sample renaiming when using dual combinational indexes for paired-end data (DEMULTIPLEX)
minBoot option fixed in DADA2 taxonomy annotation
vsearch quality filtering “minsize” not working (option currently removed).

Implemented software: