amptk v1.2.5

• bug fix where edlib version was not properly parsed due to changes upstream, fix is backwards compatible and hopefully future version compatible as well. This was error in #40 and several other "offline" emails.
• update to amptk stats to generate interactive html output for NMDS output, allowing users to identify which samples correspond to which point on the graph. This requires r-plotly, r-htmltools, and r-dt -- however should be all installed through bioconda
• bug fixes for amtpk SRA-submit
• improve error/logging in amptk taxonomy
• fix R scripts to be compatible with R>3.4.1 -- somehow different way of parsing the command line arguments. Also removed the "auto-install" function in the R scripts -- this was meant to be a convenience but didn't always work.

amptk v1.2.4

• trying to fix tab error that bioconda didn't like, version bump accordingly.

amptk v1.2.3

• fix auto-detect of base name output files in clustering scripts
• bump version
• update citation as now published in PeerJ https://peerj.com/articles/4925/

amptk v1.2.2

• fix tab indentation bug for py3
• add minimum length and trimming length to log file and terminal output.

amptk v1.2.1

• numerous bug fixes: including a fix for --require_primer off in amptk illumina. Several bug fixes in amptk illumina2 and amptk illumina3 pre-processing steps.
• thread (processes) control added for clustering steps

amptk v1.2.0

• for all Illumina pre-processing methods the order of steps has been changed to now 1) search for primers/trim and then 2) merged PE reads. This ensures that all primer/adapter sequences are trimmed from dataset, whereas previously AMPtk releases merged PE reads first - because of how usearch/vsearch merge PE reads, occasional primer/adapter sequences were slipping through the pre-processing steps. Also reads with multiple primer hits (i.e. two forward primers) are now discarded. While this results in the pre-processing steps being slightly slower in runtime, it increases the data quality downstream.
• read orientation is tested/fixed on the fly for amptk illumina2 workflow (barcodes/primers in reads). Some datasets of 50/50 read orientation.
• added a check for "inverted OTUs" for all denoising/clustering steps. This was largely a check to validate that changing illumina pre-processing steps were working correctly (as unintended result was a small number of OTUs that were on the "crick" strand)
• Default mapping file now has a 'RevBarcodeSequence' column. Mapping files used for amptk illumina2 enforce the paired barcode sequences in the mapping file. If barcode fasta files are given, then all combinations of barcodes (5' and 3') are saved.
• a few py27/36 bug fixes

amptk v1.1.3

• update to amptk taxonomy to alert user if sample names are duplicated
• many fixes to unify the 'base name" output for many scripts
• remove colored date/time stamp for all platforms except Mac
• many fixes for py2/py3 compatibility
• amptk now moved to bin directory - will slightly change install

amptk v1.1.2

• update compatibility for py2/3

amptk v1.1.1

• bug fixes for amptk lulu, bug fixes for amptk taxonomy to better deal with 16S 8 level taxonomy
• added some minor functions to amptk filter
• improvement of amptk illumina3 as well as allowing --barcode_rev_comp to reverse complement barcode sequences, i.e. if indexing was done on reverse primer. mapping file is not required now can also pass primers and a barcode faster file for demuxing.
• clean up repo slightly, trying to get conda recipe working.

amptk v1.1.0

• bug fix for amptk filter and the subtract feature #31
• fix menu option #33
• added LULU module for OTU curation, see more here: https://www.nature.com/articles/s41467-017-01312-x
• LULU usage: amptk cluster --> amptk filter --> amptk lulu --> amptk taxonomy --> amptk stats
• added indicator species analysis to amptk stats
• several bug fixes for amptk stats
• added option to drop specific OTUs prior to running amptk stats