Skip to content
This repository has been archived by the owner on Nov 9, 2023. It is now read-only.

QIIME 1.9.0
Compare
Choose a tag to compare
@gregcaporaso gregcaporaso released this 30 Jan 21:33
· 192 commits to master since this release
1.9.0
b02ff7d

We're excited to announce QIIME 1.9.0. As is typical for our releases, the QIIME 1.9.0 Virtual Box and EC2 image will be ready in about a week.

Installing QIIME 1.9.0

The easiest way to install QIIME is by using pip. You can find the instructions for doing this in our (completely updated!) install document. See our updated upgrade documentation if you'd like to upgrade a pre-existing QIIME installation.

About QIIME 1.9.0

QIIME 1.9.0 contains a huge amount of new features. Some of the highlights include:

  • Beta support has been added for open source alternatives for all OTU picking algorithms (de novo, closed-reference, and open-reference, including subsampled open-reference). These make use of SortMeRNA for closed-reference steps, and swarm and SumaClust for de novo steps. Open reference OTU picking with these tools can be accessed with pick_open_reference_otus.py -m sortmerna_sumaclust.
  • Added three new workflow scripts for facilitating initial QIIME processing of already-demultiplexed fastq files, as these are commonly being provided by sequencing centers. These are: multiple_split_libraries_fastq.py, multiple_join_paired_ends.py, and multiple_extract_barcodes.py. We've re-written our Illumina Processing Documentation to describe these, and some other scripts, that will help you process raw Illumina data.
  • Added new observation_metadata_correlation.py script. This script allows the calculation of correlations between feature abundances and continuous-valued metadata. This script replaces the continuous-valued correlation functionality that was in otu_category_significance.py in QIIME 1.7.0 and earlier.
  • Added new compute_taxonomy_ratios.py script, which implements the microbial dysbiosis index (MD-index) from Gevers et al 2014.
  • Added collapse_samples.py, which can be used for collapsing groups of samples in BIOM tables and mapping files based on their metadata (see #1678). This can be used, for example, to collapse samples belonging to a replicate group. This also has replaced summarize_otu_by_cat.py (see discussion on #1798).
  • Added differential_abundance.py to supplement group_significance.py which supports metagenomeSeq's fitZIG algorithm and DESeq2's negative binomial algorithm. Similarly, we added normalize_table.py to support normalization algorithms in addition to rarefaction. Supported methods are metagenomeSeq's CSS and DESeq's variance stabilizing transformation.
  • Added script compare_trajectories.py, which provides access to analysis of volatility using different algorithms.
  • Added script start_parallel_jobs_slurm.py, which allows for parallel job submission using slurm.
  • Updated a lot of our web documentation, including the 454 Overview Tutorial, the Illumina Overview Tutorial, the EC2 tutorial, and the QIIME script index.
  • Greengenes 13_8 is now installed as part of the QIIME base install, and the 97% reference OTUs are used as the default reference database for the OTU pickers and taxonomy assigners. This is convenient for users working with 16S data, and can easily be overridden for users working with other marker genes. This means that all of the QIIME workflows can be run immediately after pip installing QIIME - there is no need to download other files or create a qiime_config.

This is just a sneak-peek at some of the new features that are packed into QIIME 1.9.0. See the ChangeLog for a lot more detail.

Finally, thanks to all of the QIIME developers for the huge amount of effort that went into this new release, and to our users for using QIIME and for testing the 1.9.0 release candidates.

Assets 2
Loading