All notable changes to this project will be documented in this file.
This project tries to adhere to Semantic Versioning.
For version numbering, we use the following convention: MAJOR.MINOR.PATCH.
Each element increases numerically (e.g., 1.9.0 -> 1.10.0 -> 1.11.0).
- New
seqstatssub-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_replicatesparameter (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)
- 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
- 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 artefacts 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
- Add Ilumina-based workflow (see
--seqplatformflag) - Publish Singularity image to Singularity library
- Minor bugfixes in
primer_check(multiprimer artefacts),pool_seqs(sequence headers), andprep_asvtab(aggregation of non-unique joined Illumina sequences) processes - New logo design (thanks to Olesya Dulya)
- Initial release