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@vmikk vmikk released this 22 Jan 12:39
· 28 commits to main since this release
1.1.0
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vmikk Vladimir Mikryukov
GPG key ID: E04480F646218BC6
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Learn about vigilant mode.
f0199fb
This commit was signed with the committer’s verified signature.
vmikk Vladimir Mikryukov
GPG key ID: E04480F646218BC6
Verified
Learn about vigilant mode.

NextITS v.1.1.0 [2026-01-22]

  • Fixed handling of unknown barcode combinations (in dual asymmetric mode); thanks to Alice Retter for reporting
  • Refactored and optimized the tag-jump removal step
  • Fixed a bug with duplicated sequences in the tag-jump removal step; thanks to Valentin Étienne for reporting
  • Implemented a chunking option for splitting the dataset into smaller parts prior to clustering in Step-2 (pre-clustering, clustering, and denoising moved to a separate sub-workflow), using MMseqs2
  • Added possibility to disable reference-based and/or de novo chimera removal steps and tag-jump removal
  • New parameters added:
    • lima_remove_unknown (default, false; if true, unknown barcode combinations are removed from demultiplexed data)
    • chunking_n (number of chunks to split the dataset into prior to clustering)
    • chunking_id (minimum sequence identity used for splitting the dataset into chunks)
    • chimera_methods (specifies which chimera removal methods to use - "ref" for reference-based, "denovo" for de novo, or "ref,denovo" for both; could be also "none" or null to disable chimera removal)
    • tj (specifies whether to run tag-jump removal - "true" or "false")
  • Added DADA2 denoising (--preclustering dada2; also works with --clustering none)
  • Implemented automated documentation for analysis procedures (generates README_Step1_Methods.txt and README_Step2_Methods.txt in the pipeline_info directory)
  • Refactored parameter validation (using nf-schema plugin)
  • Refactored the runtime parameter summary and help message
  • Added test profiles (test, test1, test2)
  • Improved run summary for Step-1
  • Default parameters changed:
    • ITSx now checks only a single strand (option ITSx_complement set to F). This should be safe for most cases, as amplicons were re-oriented using primers during the pipeline run. However, we recommend checking the results carefully (e.g., columns ITSx_Extracted_Reads and ITSx_Yield_Percent in the run summary)
    • Prior to tag-jump removal, sequences are now dereplicated at 100% identity (option tj_id set to 1). It is possible to pre-cluster sequences at a lower similarity threshold (e.g., --tj_id 0.99) but this will take much longer. This change should also be safe for most cases, as amplicons undergo homopolymer-correction
  • Fixed a minor bug in extraction of sample IDs at the ref-based chimera rescue step; thanks to Valentin Étienne for reporting
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