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Improved support for very long fasta sequences (e.g. full chromosomes), even for multiple sequences per file. This is done by relying on an external .fai index, which is now necessary for sequences with unbounded length.
File input formats can now be mixed (e.g. fastq, fasta, long fasta can be read by the same job).
k-mer statistics can now optionally be written to an output file using a new argument (not just to standard output as before).
For convenience, additional PASHA minimizer sets for k >= 19, m=10,11 were added to the distribution.