VERSION=25.12 + replacement of SAM2MSA with CoPro for computing the genome coverage profile + replacement of Prokka with Bakta for genome annotation + Bakta and Platon are now optional + tested with the last versions of: AlienTrimmer, AlienDiscover, contig_info, Platon, samtools, SPAdes + strategy -s B now runs only Bakta; new strategy -s G to run both Bakta and Platon + new option -e to run SPAdes with a complete range of k-mer lengths + modified default Phred score cutoff, i.e. -q 13 + modified default MINCOV, i.e. -c 2 + coverage confidence interval set to 99.99% + modified MINDFREQ=0.666 to assess multi-allelic positions + a second step N is run when the first one leads to a too large coverage depth + updated parameters for the two polishing steps + print md5 of each input FASTQ file + new accuracy := momo * R2