JAMP v0.79

• Updated Cluster_otus function to now work with >1000 files. Merging files for clustering is now done in chunks of 100.
• Minor bug fixes in the tutorial file package_tutorial.R.
• Added logo and a bit of documentation

JAMP v0.78

• Fixes crash caused by fastq flag now getting ignored in cutadapt. Make sure to update to the latest cutadapt version.
• Updated the tutorial to use Vsearch instead of Usearch.

JAMP v0.77

• Denoising now works with Vsearch
• TilePlots improvements
• Improved support for truncating and clustering using Vsearch

JAMP v0.76

• map2ref and max_ee now also work with exe=vsearch.
• updated tutorial files.
• various minor bug fixes and improvements in reporting (a lot actually :).

JAMP v0.75

• Various bug fixes for the Denoising function (handles empty files better).
• Denoising now includes heat map generation.

JAMP v0.74

• For Cutadapt the error rate (error=0.1) can now be customized, and ambiguities in sequences can be resolves, e.g. to cope with Ns caused by sequencing errors (ambsequ=T).
• Plots of sequences lost are now scaling proportionately with sample name length.

JAMP v0.73

• new universal function PE_merge() that supports merging reads with usearch or vsearch. Default is vsearch, but can defined with exe. Additional PE merging software is planned in the future.

JAMP v0.72

• Speed improvements in taxonomic assignment and minor bug fixes.

JAMP v0.71

• Initial release of buildCustomdb to build your own custom databases.

JAMP v0.70

• various minor bugfixes in minmax, cutatap, map2ref.
• Initial release of buildBOLDdb, allowing to convert BOLD reference sequence TSVs to a reference data fasta and taxonomy file.
• Initial release of assign_taxonomy, allowing to use JAMP formatted reference databases to assign taxonomy to fasta files.