- added preprocessing of raw reads
- added
--preprocessedflag to suppress preprocessing for already preprocessed datasets - R1/R2 read lengths are now assessed and homogenised separately (i.e. they can have different lengths as supported by Figaro)
- initial read length distribution assessment is now performed by fastqc
- fastq filenames are normalised to R1/R2 naming scheme
- readlen homogenisation is now performed by bbduk
- added mapseq-profiling of asv sequences
- added two parameters (
--dada2_chimera_method,--dada2_chimera_min_fold_parent_over_abundance) for dada2 chimera removal
Bugfixes/Workarounds
- fixed an R script error that would generate the wrong table format when having a single sample
- in
dada2_analysiscommented vortex-code (prevalence check) as it fails for certain samples