Tags

VERSION=25.03
+ fixed bug when using 3 libraries (lib3 PE read alignments for coverage profile)
+ fixed bug when creating TMP_DIR
+ debugging issue #123 by removing $TMP_DIR/aln.bam before merging (if required)
+ new accuracy index
+ tested with up-to-date dependancy versions

VERSION=25.01
+ debugging issue #123 by removing $TMP_DIR/aln.bam before merging (if required)
+ new accuracy index
+ tested with up-to-date dependancy versions

VERSION=24.02
+ improved check dependencies using option -d
+ use the more efficient unimodality (momo) index instead of the bimodality coefficient

VERSION=23.12
+ new option -d to check dependencies
+ modified default Phred score cutoff, i.e. -q 20
+ modified default MINCOV and MAXCOV values, i.e. (3,60) instead of (3,61)
+ modified estimate of the genome length, using NTCARD with k=25
+ only 1 thread for step M: slower but reproductible (FLASH output depends on the no. threads)
+ now requires SAMTOOLS v1.18
+ improved assembly polishing step for strategies A, B, P, S and V (option -s)
+ only undefined (N) position with enough coverage are written into output file .scf.amb.txt

VERSION=23.07
+ fixed bug with option -w
+ based on FQCLEANER v23.07
+ MINIMAP2 replaced with BWA-MEM2
+ less conservative genome size approximation, i.e. gsize=F0-f1-f2
+ modified default MINCOV and MAXCOV values, i.e. (3,61) instead of (2,60)
+ modified k-mer size selection for SPADES
+ fast assembly polishing step based on SAMTOOLS for strategies A, B, P, S and V (option -s)
+ new output file .scf.amb.txt