amptk v1.0.3

• update the ITS database to use newest version of UNITE database version 01.12.2017.

amptk v1.0.2

• bug fix for amptk show if non gzipped file passed it was removed
• added gzip support for amptk sample
• bug fix for amptk filter if OTUs and OTU table did not overlap 100% then script would die, added sanity check
• changed --col_order in amptk filter to be a space separated list (was previously comma separated with no space).

amptk v1.0.1

• minor bug fixes for amptk database
• update to amptk filter to only label potential chimera OTUs if --calculate all is passed, i.e. you are using a synthetic mock that won't be in the rest of your samples

amptk v1.0.0

• now requires edlib v1.2.1 -> thanks to Edlib developer (Martin Šošić) for finding the bug that was preventing full usage of edlib in amptk. primer and barcode searches now very fast.
• added a new phyloseq module, amptk stats which will run some preliminary community ecology stats on your BIOM output file. requires R and phyloseq
• added support for UNOSIE3 via the amptk unoise3 command, note you will need to have USEARCHv10 for this script to work.
• updated global alignment taxonomy search to better deal with multiple hits in the reference database
• updated ITS reference database as well as COI database.
• finally wrote some more comprehensive documents, located at http://amptk.readthedocs.io
• several minor bug fixes

amptk v0.10.3

• bug fixes for amptk database. Rewrote the dereplication function and added --lca or last common ancestor function for building the UTAX databases.
• bug fixes for amptk SRA-submit and update to edlib for searching.
• bug fix for amptk filter where samples passed to --drop are not used for index-bleed calculation
• bug fix for pre-processing and --mult_samples argument

amptk v0.10.2

• bug fix for -t, --threshold option of amptk select and amptk remove. Bug was introduced during last update when support for compressed files was introduced
• AMPtk now supports degenerate nucleotide primer matching, thanks to the very fast edlib v1.2 library. You will need to have at least edlib v1.2.0, can upgrade with pip, i.e. pip install -U edlib. The scripts will check your edlib version during runtime and let you know if you need to upgrade.

amptk v0.10.1

• bug fix for amptk filter where some mock sequences were not being annotated correctly
• upgrade amptk SRA-submit to use edlib alignment
• fix menu in several places

amptk v0.10.0

• Major update is to use edlib library for alignment, this is a dramatic increase in speed, however downside is that degenerate nucleotides are not supported in edlib currently (hoping to get this fixed soon). You can increase --primer_mismatch to allow for degenerate matches, keep in mind that currently any degenerate nucleotide will be counted as a mismatch. v0.9.3 still supports degenerate nucleotides, although the alignment is much less accurate and is 10X slower.
• edlib alignment now supports barcode_mismatches as well without a loss in speed.
• update to MergePE function, which allows user to select either vsearch or search for merging paired end fastq files, controlled via --merge_method. Update to phiX filtering to split files if >3GB to avoid memory problem in USEARCH 32 bit.
• add amptk illumina3 method for pre-processing, this will demultiplex Illumina PE files along with index read files
• support for gzipped input files, as well as now default will output fq.gz demuxed files. Save space during processing.
• updated docker container and install instructions

amptk v0.9.3

• remove bedtools as dependency for converting BAM -> FASTQ. Now AMPtk will first try to use samtools if it exists, then bedtools if it exists, and will default to pybam native python parser to convert. Pybam is 10X slower than samtools, but is written in python thus no extra dependencies needed.
• added threshold filtering to amptk remove and amptk select, so you could remove all samples with reads less than 5000 by running, amptk remove -i input.demux.fq -t 5000 -o output.demux.fq

amptk v0.9.2

• bug fix for amptk dada2 denoising where reads were getting ignored if they contained any ambiguous nucleotides. The filter for ambiguous nucleotides is still maintained prior to DADA2, note that terminal N's from padding will be properly removed, only internal ambiguous nucleotides are not allowed in DADA2