amptk v0.8.0

• package has undergone a name change to reflect changes in the scripts. Originally the project started as essentially a wrapper for UPARSE and thus relied heavily on USEARCH. Coupled with originally supporting fungal ITS sequences, it was named UFITS (usearch fungal ITS). However, the current implementation of AMPtk relies very little on USEARCH and can support any amplicon based NGS dataset. Out of the box the following DB are packaged: fungal ITS, fungal LSU, 16S, insect/animal COI. Thus I feel that amptk is a better name that describes what the scripts do.
• option -p, --pad was added for amptk ion, amptk illumina, amptk illumina2, and amptk 454 to allow user to turn off the padding with Ns to the --trim_len
• option -c,--calculate was added to amptk filter to control how the script calculates index-bleed. By default it calculates index-bleed into the mock community sample (-b) as well as out of the mock community into the rest of the samples. However, if members of the mock community are found in your samples, this calculated number is wrong, so if any members of your mock community are plausibly found in samples that you are sequencing, then you should use the --calculate in option.
• packaged databases had to be moved to a different sharing location (USDA now prevents use of dropbox), so they are now on Box, however it seems like the download speed is quite a bit slower. If anybody has recommendations for a free place to host these databases let me, need about 1 GB of space and need to be able to access with a directly link from the command line.