Contents
- 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)
Software | version |
---|---|
NextITS pipeline (link) | 0.5.0 |
ORFfinder (link) | v0.4.3 |
RDP classifier | v2.13 |
DADA2 | 1.27 |
vsearch | 2.23 |
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 |
- 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)
Software | version | Reference |
---|---|---|
DADA2 | 1.20 | Callahan et. al 2016 |
vsearch | 2.22.1 | Rognes et. al 2016 |
trimmomatic | 0.39 | Bolger et al. 2014 |
seqkit | 2.3.0 | Shen et al. 2016 |
cutadapt | 3.5 | Martin 2011 |
mothur | 1.46.1 | Schloss et al. 2009 |
ITS Extractor | 1.1.3 | Bengtsson-Palme et al. 2013 |
fqgrep | 0.4.4 | Indraniel Das 2011 |
BLAST | 2.11.0+ | Camacho et al. 2009 |
FastQC | 0.11.9 | Andrews 2019 |
MultiQC | 1.12 | Ewels et al. 2016 |
LULU | 0.1.0 | Froslev et al. 2017 |
fastp | 0.23.2 | Chen et al. 2018 |
DEICODE | 0.2.4 | Martion et al. 2019 |
- 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)
Software | version | Reference |
---|---|---|
DADA2 | 1.20 | Callahan et. al 2016 |
vsearch | 2.18.0 | Rognes et. al 2016 |
trimmomatic | 0.39 | Bolger et al. 2014 |
seqkit | 2.0.0 | Shen et al. 2016 |
cutadapt | 3.5 | Martin 2011 |
mothur | 1.46.1 | Schloss et al. 2009 |
ITS Extractor | 1.1.3 | Bengtsson-Palme et al. 2013 |
fqgrep | 0.4.4 | Indraniel Das 2011 |
BLAST | 2.11.0+ | Camacho et al. 2009 |
FastQC | 0.11.9 | Andrews 2019 |
MultiQC | 1.12 | Ewels et al. 2016 |
LULU (link) | 0.1.0 | Froslev et al. 2017 |
fastp (link) | 0.23.2 | Chen et al. 2018 |
DEICODE (link) | 0.2.4 | Martion et al. 2019 |
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).
- ASV workflow with DADA2 for paired-end data.
- vsearch based OTU workflow.
- QualityCheck module with MultiQC and FastQC
Implemented software:
Software | version | Reference |
---|---|---|
DADA2 | 1.14 | Callahan et. al 2016 |
vsearch | 2.18.0 | Rognes et. al 2016 |
trimmomatic | 0.39 | Bolger et al. 2014 |
seqkit | 2.0.0 | Shen et al. 2016 |
cutadapt | 3.5 | Martin 2011 |
mothur | 1.46.1 | Schloss et al. 2009 |
ITS Extractor | 1.1.3 | Bengtsson-Palme et al. 2013 |
fqgrep | 0.4.4 | Indraniel Das 2011 |
BLAST | 2.11.0+ | Camacho et al. 2009 |
FastQC | 0.11.9 | Andrews 2019 |
MultiQC | 1.12 | Ewels et al. 2016 |