amptk v1.60

• ITS database has now gotten too large to be hosted in single file on OSF, so its split into two. All users will need to upgrade to v1.6.0 in order for database to be properly downloaded, used.

AMPtk v1.5.5

• bug fix for amptk unoise3 #96 #99

AMPtk v1.5.4

• bug fix for amptk database that was stripping species epithet names #81
• bug fix for linux systems related to platform, fix was to use distro #91
• added action to build docker images and push to docker hub. Fully functional version can be run with shell amptk-docker script, usage see https://amptk.readthedocs.io/en/latest/index.html#run-from-docker
• Updated fungal ITS database based off of UNITE v8.3, upgrade with amptk install
• Added new PR2 database for universal SSU amplicons, https://github.com/pr2database/pr2database, add with amptk install
• Re-wrote amptk funguild instead of running the original Guilds.py script as this stopped working at some point

AMPtk v1.5.3

• typo/bug fixes #84 #85
• fix to multiprocessing so now py>3.7 working #83

amptk v1.5.2

Bug fix release

• fix for merging PE reads with vsearch
• fix dereplicate function in database #77
• fix for filter if --negatives passed but no mock community barcode
• fix for taxonomy where custom databases not working with the -d flag #80
• add -p illumina3 to SRA-submit

amptk v1.5.1

• to support OSX Catalina dropping 32-bit applications, I've removed usearch9 as a strict dependency. vsearch will be the default for all processing steps, including taxonomy assignment. Along these lines, I've dropped UTAX classifier as "default" in the hybrid taxonomy method.
• dropping usearch, required addition of a few new dependencies: mafft, fasttree, and the python package pyfastx (for speed simplicity).
• added support for PacBio CCS reads. Reads can be processed with amptk pacbio and then clustering with amptk pb-dada2
• several bug fixes
• fix embarrassing typos in v1.5.0 -- do not use v1.5.0 its broken.
• apparently it does not work in python 3.8 -- investigating that for future release/support.
• working on ONT (Oxford Nanopore) support as well -- stay tuned for this in near future.

amptk v1.4.2

• add --pseudopool option to amptk dada2

amptk v1.4.1

• bug fix for amptk summarize if taxonomy not present #57
• add FASTA extraction step to install #59
• add chimera detection options to dada2 #60
• fix DADA2 for ion torrent data, in newer versions of dada2 the quality score issue has been fixed, so can now use quality scores during sample inference.

amptk v1.4.0

• fix for amptk summarize --> rewrote script
• large update to taxonomy assignment, switched to vsearch for all global alignment steps
• update to all taxonomy databases, the downloads are larger but the data should be more robust
• update to the COI bold2utax method in docs
• update to amptk database and the command line options
• bug fixes along the way

AMPtk v1.3.0

This is a major reorganization of the code so it is "properly packaged" and can be installed with pip and hopefully conda. After v1.2.4 there were apparently changes to conda that would not allow the scripts to build with the previous code organization. I've then also fixed a few of the bugs that have shown up more recently, including:

• The py2 error in the bold2amptk.py accessory script #40
• the edlib version bug reported several times after edlib updated how it stores the version info #46