JAMP v0.69

• Various denoising bug fixes
• Bug fix, caused with PE merging name detection in rare cases

JAMP v0.68

• map2ref - added options for number of threads for usearch.
• add option to keep short sequences when truncating.
• bug fix - cutadapt no longer crashes when trimming fasta files.
• Temporary hot fix, clustering now works on 1000+ individual files (limit with the cat command).
• Denoising now works on individual files.

JAMP v0.67

• map2ref now supports minuniquesize so e.g. singletons can be removed before mapping against a specific reference database.
• Default heatmap colors have been improved.
• mep2ref can now use dereplicated files as input files.
• Bug fix: U_subset and map2ref now correctly process files supplied in files.
• Bug fix: Fixes a problem where map2ref would crash due to issues with removing the NULL row when generating the hit table.

JAMP v0.66

• universal path for denoising exe
• OTU clustering now honors size information in input files (works now with dereplicated data as input files)

JAMP v0.65

• update cutadapt path in minmax

JAMP v0.64

• Added flexible path for cutadapt

JAMP v0.63

• SRA() now reports file renaming.
• SRA() now correctly names illumina reads with R1 and R2 to facilitate PE merging.

JAMP v0.62

New features:

• New function to download sequence data from NCBI SRA! -> SRA(), needs the NCBI SRA Toolkit installed!
• Raw data for sequence length distribution is now saved as well.
• The bold web hack no longer shows count data for each taxon.
• Demultiplexing_index Now can deal with empty files, and stops if file names are duplicated.
• Statistic files and plots of most functions have now the folder ID included, so they can be easyer extracted from different folders.

Bug Fixes:

• The function to plot sequence length distribution now also works if the file contains only a few sequences.
• U_fastq_2_fasta() can now deal with files that have fastq in the file name.
• The bold web hack now ignores taxa named "NA"

JAMP v0.61

• Fixed a bug in Map2Ref that would save the wrong sequences if "keep only hits" was enabled.
• Fixed a bug where heatmaps would not be plotted when filtering was disabled in OTU clustering.
• When PE merging data, length distribution data is now saved as well (unless skipped).

JAMP v0.60

• Fixes bug in demultiplexing indexed if md5 is skipped
• Now allows empty files in map2ref