JAMP v0.49

• Path to usearch executable can now be specified in all functions that use usearch.
• In rare cases a low abundant OTU can end up receiving no reads in mapping, causing a crash of the program. This bug was resolved.
• Fixed a bug in OTU plotting that would generate warnings in some circumstances.

JAMP v0.48

• New FastQC module to generate summary stats of individual fastq files.
• New module for demultiplexing raw data with illumina index files present (Demultiplexing_index).
• When removing primers with cutadapt, inosine is now automatically converted to N.
• sequences can now be truncated to a specified length in U_truncate. Additionally one can choose to not rename the output files (useful when PE merging is desired afterwards).
• Minimum overlap can now been set in PE merging.
• Improved log files (PE_merging).
• Bug fix, FastQC now handles gz compressed data correctly.

JAMP v0.47

• Plotting length histograms is now skipped for empty files. Additionally, the number of sequences is indicated in the figure title.
• EE filtering now deals with empty files, and warns, if files are empty or all sequences from a files, are discarded while filtering.
• Also fixes a bug in OTU clustering, where heatmaps where not generated correctly with filter=NA.
• Some spelling mistakes are fixed in reporting.
• Some functions give now the median of reads retained, instead of just the average.

JAMP v0.46

• Improved colors in heatmaps
• BETA: OTU clustering can now handle empty files (other functions still need to be adjusted when producing summary statistics).

JAMP v0.45

• Added a new function map2ref allowing to map reads directly against a reference database.
• Added an option where primers can be trimmed with cutadapt without being anchored to the 3/5' ends (anchoring=T).
• Fixed a bug that caused fastq2fasta to crash.
• Fixed minor bugs in PE merging, where in some cases fastq files were not renamed and "R1" retained in the sequence name (only a cosmetic problem).

JAMP v0.44

• Added a new function length_distribution() to plot the sequence length distribution in fasta and fastq files.
• The read length distribution can be plotted with LDist=T when using U_merge_PE(), Cutadapt(), or Minmax().

JAMP v0.43

• Added new function Sequences_lost() to plot how much sequences were discarded in a processing step. please see wiki for documentation how to use it.
• When running the modules U_merge_PE(), Cutadapt(), Minmax(), U_max_ee() and U_subset() bar plots are generated in the _stats-folder indicating the amount of sequences discarded.
• Demultiplexing_shifted() now includes a bar plot showing the distribution of demultiplexed sequences.
• U_subset now reports the amount of sequences discarded.

JAMP v0.42

• Bug fix, forgot a -

JAMP v0.41

• Added a new function to visualize OTU tables as heatmaps OTU_heatmap(). See wiki for more info.
• The U_cluster_otus() function does now automatically heatmaps for raw and filtered data.

JAMP v0.40

• U_merge_PE Paired end merging now accepts fastq files that end in txt or fastq.
• Added an option bothsides=T to Cutadapt, where the reverse complement of each sequence is also searched for the respective primer pair. This can be useful, if your sample is sequenced from both orientations in parallel (e.g. when libraries are prepared with the TruSeq kit).
• Added an function to delete the last folder, including it's entries in the log file.
• New function to barplot haplotype distribution across samples Denoise_barplot(). A plot is also automatically generated when using Denoise(). Please see wiki for details.
• Updated the tutorial files to reflect the new changes.