[Preview] QIIME 2 2023.9 development changelog

Developer Discussion
1

QIIME 2 2023.9 has been released!
Please see the official changelog for more details.

Original content of post

:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2023.9

This post is a live-document which will be updated throughout our development cycle. Any links will in this topic will be broken until the release is officially published. When we are ready for release, we’ll copy this changelog and create a new post in the Announcements category .

Developer Project Board:

QIIME 2 2023.9 Project on Github

:bangbang: Important Announcements :bangbang:

  • New QIIME 2 distributions :tada: :tada: :tada:

    • We are extremely excited to share that we are released three QIIME 2 distributions in 2023.9. A QIIME 2 distribution is a collection of plugins that are designed to work together, and which are grouped around some theme.
    • As of 2023.9, the QIIME 2 core distribution is referred to as the QIIME 2 Amplicon Distribution. This reflects that this collection of plugins is designed to support microbiome marker gene amplicon data analysis (e.g., 16S, ITS, COI, 18S, ...).
    • We have additionally released our first, alpha release of the QIIME 2 Shotgun Distribution, a collection of plugins designed for supporting microbiome shotgun metagenomics data analysis. This workflow supports end-to-end shotgun metagenomics analysis, including functional and taxonomic identification of reads, and assembly of contigs and metagenome-assembled genomes. This should be considered a test release, and should yet not be used for real-world data analysis. We are releasing this to begin collecting feedback from early users on what works well, what doesn't, and what else should be included. We'll be releasing more details in the form of tutorials shortly. We are particularly interested in hearing about how results generated with the QIIME 2 shotgun analysis workflow compare to results generated with your standard workflow, so please feel free to share!
    • Finally, we released the QIIME 2 Tiny Distribution. This is a minimal set of QIIME 2 functionality for building and using plugins through the QIIME 2 command line, and is intended for use by developers who want a minimal QIIME 2 environment to work in.

  • q2-gneiss - DEPRECATION NOTICE :no_entry_sign:

    • gneiss is no longer actively maintained, and q2-gneiss has been fully removed from the QIIME 2 Amplicon distribution.

Here are the highlights of the release:

  • qiime2

    • @Oddant1 Added support for kebab-case-keys to the artifact cache :oden:
    • @colinvwood integrated the functionality of provenance_lib, which was previously a standalone package in the qiime2 environment, into the qiime2 framework and the cli. The original software was developed by @ChrisKeefe.

  • q2-demux

    • @Oddant1 Added actions to partition demultiplexed sequences into collections of smaller artifacts :heavy_division_sign:
    • @crusher083 Fixed some deprecation warnings :warning:
    • @gregcaporaso added the tabulate-read-counts action, which generates an ImmutableMetadata artifact from various demultiplexed sequence type that describes the number of reads observed per sample. This information was previously only available in the summarize visualization, making it hard to integrate this information in downstream analyses (e.g., to color points in a PCoA plot based on how many sequences were obtained for them).

  • q2-diversity

    • @gibsramen and @wasade added support for a modified Procrustes analysis wherein a computed transformation can be fit on two ordinations and then applied to additional points :point_up_2:t3: :chart_with_upwards_trend:

  • q2-feature-classifier

    • @Nicholas_Bokulich Enabled optional use of pre-indexed databases with blast :boom:
    • @isaiah-ghost added optional Metadata and Collection[FeatureData[Taxonomy]] to the tabulate-seqs visualization. This simplifies comparing the results of multiple taxonomy assignment approaches (such as different databases), and putting that information along side the sequence for easy BLASTing, to see what NCBI thinks. More feature information is coming soon to this visualization. Happy feature exploring! :1234::microbe:

  • q2-feature-table

    • @gregcaporaso Added the ability to merge FeatureTable[PresenceAbsence] :face_in_clouds:

  • q2-quality-control

    • jordanrabasco added decontam-indentify-batches - a new pipeline action which subsets a table, runs decontam on the table subsets and then visualizes those tables in an easy to read graphic :bar_chart: :partying_face:

  • q2-types

    • @lizgehret Migrated FeatureMap from q2-types-genomics to q2-types :heavy_plus_sign:

  • User Docs :books:

    • @lizgehret updated installation instructions and details on each of the new QIIME 2 Distributions :globe_with_meridians:
    • Thanks to @crusher083's suggestion, our install instructions now include the use of mamba for environment creation, which will drastically improve on installation time compared to conda :snake: :nerd_face: