v.0.5.0 [2023-08-08]

• New seqstats sub-workflow (only dereplication, primer validation, and basic run stats)
• Add SWARM clustering (Mahé et al., 2022 DOI:10.1093/bioinformatics/btab493)
• Add post-clustering curation with LULU (Frøslev et al., 2017 DOI:doi.org/10.1038)
• Add barcode validation step
• Add SSU and LSU region-based output sequences
• Add support for UNOISE-only output (without clustering)
• Add merge_replicates parameter (Step-2) for merging or keeping separate sample replicates
• Update Step-1 run summary (add homopolymer stats)
• Deprecate taxonomy annotation workflow at Step-1
• Fixed different extensions in demultiplexed input
• Experimental: UNITE-style dereplication (allows query sequences to vary in length at 100% similarity)
• Experimental: support of alternative alignment penalty scores (ITS-specific feature)

v.0.4.0 [2023-05-08]

• Add Step-2 workflow for pooling, dereplicating, and clustering sequences from Step-1
  • Read clustering with VSEARCH (Rognes et al., 2016 DOI:10.7717/peerj.2584)
  • Error-correction with UNOISE2 (Edgar, 2016 DOI:10.1101/081257)
• Add run summary for Step-1 (read counts at different pipeline stages)
• Separate config for HPC clusters
• Add Docker container

v.0.3.0 [2023-03-02]

• Add support for pre-demultiplexed data as input
• Add option for semi-full-length ITS (especially useful when forward primer is located at the very end of SSU and the HMM site can not be recognized by ITSx)
• Add removal of long homopolymer artifacts at QC stage
• Correct handling of a case with no valid sequences at primer checking step (thank to Taavi Riit for reporting the bug)
• Bug fixed in assemble_its (thanks to Kadri Põldmaa for discovering the error)
• Addition of ITSx detailed results (with information on the HMM profile used for ITS extraction)
• Fixed sample names for the rescued chimeric sequences
• Minor fixes related with the Singularity container, output directory, help message, and single-end QC

v.0.2.0 [2022-09-30]

• Add Ilumina-based workflow (see --seqplatform flag)
• Publish Singularity image to Singularity library
• Minor bugfixes in primer_check (multiprimer artefacts), pool_seqs (sequence headers), and prep_asvtab (aggregation of non-unique joined Illumina sequences) processes
• New logo design (thanks to Olesya Dulya)