Bugfix in parallel cutadapt

• fixed bug in multithreading when using cutadapt
• made sgRNA enrichment/depletion analysis more efficient for increased speed

Improvements in speed and plots

• parallelized adapter trimming
• accelerated alignment analysis
• legends independent from transparency level in plot
• option to highlight genes in correlation plots
• misc minor improvements in plot colors & layout

Speed up and graphical improvements

• Option to round raw counts
• Improved plotting
• Skip numbering of samples if there are no replicates
• Auto-correct spaces in sample names
• Include average logFC in gene list
• Improved adapter trimming (wildcard at end of adapter)
• Increase speed of aRRA computation

Bug fix in case of no significant hits

• Bug fix in p-value plots in case there are no significant hits

Depletion screen bug fix

• bug fix in sorting the gene list in depletion screens
• minor bug fix in Gini coefficient calculation
• more efficient ES computation
• better visualization in read depth plot
• added p-value threshold for aRRA computation to configuration file

Sequence QC

• Integrated fastqc for sequence quality control
• Optimized Read Depth plot

Minor improvements

• Minor improvements in plot labeling and text output

Parallelized alignment

• Bowtie2 runs in parallelized mode with the maximum number of cores on the machine, leading to significant alignment speed-up
• changed the legend on the scatterplots to indicate the FDR

Minor bug fix

• Bug fix for running with only 1 control replicate
• replaced "adj. p-value" with "FDR" in output sheets

New normalization option

• added "total normalization" as another normalization option (used e.g. in MAGeCK)
• minor graphical improvements in scatterplots