Version 5.1.1

Version 5.1.1 of NGSEP. Main changes:

• New function to calculate statistics of genome assemblies
• MultisampleVariantsDetector. Implemented multithreading. New option to specify the number of threads.
• SingleSampleVariantsDetector. Implemented multithreading. New option to specify the number of threads.
• SIH. New option to output a bam file with assignments of aligned reads to haplotypes.
• TransposonsFinder. The output is now a prefix to output multiple files.
• TransposonsFinder. New option to activate the deNovo identification of TEs. The current version implements a new algorithm to identify conserved LTRs.
• TransposonsFinder. New options to control the kmer length for the de-novo algorithm, the kmer length for the search algorithm and the window length for the search algorithm.
• Diversity statistics. Included Fisher exact test for departure from HWE.

Version 5.1.0

Version 5.1.0 of NGSEP. Main changes:

• FastqFileFilter: New option to provide a file with read ids to select.
• GenomesAligner: New option to skip the synteny analysis.
• TransposonsFinder: New option to limit the length of genome sequences analyzed together.
• ReadsAligner and Assembler: New algorithm for chaining of kmer hits.

Version 5.0.1

Version 5.0.1 of NGSEP

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

VCF Converter: Added option to export to the GenePop file format
Genomes Aligner: Added option to select one genome as reference and sort and orient contigs of the other genomes according to the reference.

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

Implemented most functionalities available in the command line
Updated javafx to version 17 for mac users