Version 5.0.1

Version 5.0.1 of NGSEP. Main changes:

• New command FastqFileFilter to filter raw reads by length and average quality
• New command TransposonStats to calculate statistics of transposable elements annotated with the TransposonsFinder command
• Assembler: Added option -q to select reads based on a minimum average quality
• Assembler: Added option -mpl to select reads based on a minimum average quality

Version 5.0.0 of NGSEP.

To commemorate 10 years of NGSEP we started version 5. These is the main progress for this version

• Improved the algorithm for de-novo assembly.
• New functionalities for sorting and circularization of contigs in genome assemblies.
• Implemented more algorithms for hierarchical clustering.
• Integration with Synvisio for visualization of synteny
  See further details in the CHANGELOG

Version 4.3.2

• VCFConverter: Added option -genepop to export to the GenePop file format
• GenomesAligner: Added option -r to select one genome as reference and
  sort and orient contigs of the other genomes according to the reference
• GenomesAligner: Fixed clustering error for families with large numbers of
  paralogs
• TransposonsFinder: Added strand information to the output

Version 4.3.1

New functionalities for annotation of transposable elements and masking of genome assemblies
Improved memory management of the long reads genome assembler
Multi threading for the genomes aligner

Version 4.2.1

• Assembler: New options -cml and -cmof to set the maximum contig length and a catalog of start sequencs for circularization
• Assembler: Switched the default consensus algorithm to Polishing
• SingleSampleVariantsDetector: Added flag -runLongReadSVs to run a new algorithm for detection of structural variants from long reads
• GenomesAligner: Added option -yh and -yd to control the minimum number of units and the maximum distance between units in an output synteny block.
• GenomesAligner: Changed default values for the k-mer length and percentage of k-mers.