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2.1.3 (2024-11-14)

  • fixed bug in Issue 56 that caused some FASTQ files generated by PacBio to raise an error during validation. these files now pass validation and the interleave check has been modified from raise a warning not an error.
  • Updated the citations.bib file to include the new Microbiology Spectrum article for ITSxpress

2.1.2 (2024-9-23)

  • Fixed bug Issue 54 that caused --tempdir input to be ignored in the ITSxpress CLI and updated q2_itsxpress.py and test code for this change.
  • updates to Dockerfile
  • updates to changelog formatting and readme

2.1.1 (2024-9-19)

  • Changed settings to allow FASTQ quality scores up to 93. This prevents an error in processing some reads from PacBio, Nanopore and Element Biosciences AVITI sequencers with quality scores over 41.
  • Updated from manual software versioning to automated versioning based on git tag metadata and setuptools-scm.
  • Updated Github action workflow for QIIME 2024.5 and Python 3.9.19
  • Improved and updated installation instructions in the README file
  • Updated tests for FASTQs with high qual scores
  • Added citation information for forthcoming ITSXpress version 2 publication
  • Cleaned up some PEP formatting

2.1.0 (2024-4-10)

  • HMMs are updated to version 2 of the HMM database curated by Henrik Nilson at the University of Gothenburg.
    -Version 2 (see https://github.com/USDA-ARS-GBRU/ITS_HMMs) -5 April 2024

    New Updates to models A, D, E, F, O, P, R to improve support for oomycetes and fungal taxa with deviant ribosomal genes, notably Wickerhamiella, Calocera, and Mucoromycotina fine root endophytes

    Addition of Y.hmm to support Parabasalia

  • Added option of Y.hmm to ITSxpress standalone and Qiime2 plugin

  • Added documentation for Apple Silicon chip support.

2.0.2 (2024-3-20)

  • Fixed a bug where the 3' end of the ITS region was not being trimmed from both forward and reverse reads if the read extended past the ITS region. This was due to the trimming being done at the start of both forward and reverse reads and not the end of each read. Thus if the read overlapped the opposite end of the ITS read, part of the conserved region would still be found on the ends of the forward and reverse read. This was fixed by trimming to just the ITS region for both forward and reverse reads. This bug did not affect the results of ASV calling with Dada2 because Dada2 ignored sequences beyond the ITS region. This fix will make the output more consistent with expectation.

  • Fixed a bug for submodule logging, where submodules were not logging to the main log file. This was fixed by passing the log file to the submodules and having them write to the same log file. This issue was introduced in version 2.0.0.

  • Added unit test to confirm that the 3' end of the ITS region is being trimmed from both forward and reverse reads.

2.0.1 (2023-11-07)

Fix single-end logic bug, which looked for a reverse read file even if single-end reads were provided because the single_end flag wasn't indicated by user.

Fix unit test bug, which was failing because the test data was interleaved and the test was expecting single-end reads. This was due to the logic bug mentioned above being fixed.

2.0.0 (2023-06-28)

Release Highlights

  • Removed BBmap dependency
    • BBmap scripts are no longer used in the pipeline, including:
      • reformat.sh (interleaved files no longer supported)
      • bbmerge.sh (merging of paired-end reads now done with Vsearch --fastq_mergepairs)
        • merging of paired-end reads is different between Vsearch and BBmerge, so results may differ
  • Updated de-replication step for newer versions of Vsearch
    • Dereplication step now done using Vsearch --fastx_uniques (derep_fulllength command no longer supports fastq files)
  • Qiime2 plugin version of ITSxpress is now part of the standalone package of ITSxpress
    • No longer need to install q2-itsxpress separately and will be installed if Qiime2 is already installed, otherwise only the standalone version will be installed
    • Qiime2 plugin version of ITSxpress is no longer maintained after q2-itsxpress v1.8.1
  • Pacbio sequences are now supported if fastq file scores are in Illumina format Bug Fixes
  • Fixed bug where the q2-itsxpress plugin was not handling single-end reads correctly, and was looking for a reverse read file

1.8.1 (2023-06-02)

Release Highlights

  • This is the final version that uses BBmap scripts. The next version will remove the BBmap dependency and use Vsearch for all steps.

    • This version can still be found on the EOL-1.8.1 branch of the repository

  • Replaced derep_fulllength with fastx_uniques command compatible with Vsearch>=2.21.1

  • Fixed version of dependencies

  • Updated pip install config file to pyproject.toml

  • Updated readme usage section to reference compatible Qiime2 version

  • Added read count output to log file

1.8.0 (2019-12-9)

  • Added support for primer sets in the reverse orientation
  • Fixed a bug that could cause crashes when an intermediate file was empty

1.7.2 (2018-11-8)

  • This release fixes issue #8
    • This issue caused ITSxpress to incorrectly trim about 0.2% of read pairs. Sometimes this would result in it writing blank fastq records which would cause Qiime to detect an error and stop processing.

1.7.0 (2018-09-12)

New Features:

  • Support for the output of unmerged paired end files. This allows users to use Dada2 for sequence variant calling.
  • The API is now documented at ReadTheDocs

1.6.4 (2018-7-26)

  • Fix for issue validating fastq.gz files that was not solved by v1.6.3

1.6.3 (2018-7-25)

  • Fixed issue validating fastq.gz and added tests.

1.6.2 (2018-7-25)

  • This release fixes an error that occasionally occurred when validating FASTQ files. ITSxpress used BBtools reformat.sh which occasionally threw an exception when validating FASTQ files due to a race condition. FASTQ file validation is now done with Biopython instead.

1.6.1 (2018-7-19)

  • Changed the default clustering identity to 99.5%.
  • Experiments with fungal soil samples showed that ITSxpress and ITSx trimmed 99.822% of reads in the ITS1 region within 2 bases of each other and 99.099% of reads in the ITS2 region within 2 bases of each other at 99.5% identity. For higher accuracy, de-replication can be run at at 100% identity.

1.6.0 (2018-7-13)

  • This release adds a new feature to cluster merged sequences at less than 100% identity. This speeds up typical dataset trimming by about 10x over previous versions depending on the sample, without major effects on trimming accuracy. This feature is controlled with the --cluster_id flag. Default behavior is now to cluster at 0.987 identity.

1.5.6 (2018-7-3)

  • Database is now included in the release

1.5.4 (2018-6-27)

  • Fixed bug in handling of temporary files files specified with the --tempfile flag
  • updated readme
  • fixed issues with exception handling

1.5.2 (2018-6-21)

  • Fixed an indexing error causing ITS trimming to be off by 1 base.
  • Fixed error when raising file not found exception
  • removed old readme