Provided by: assemblytics_0~20170131+ds-2_all
Assemblytics - detect and analyze structural variants from a genome assembly
Assemblytics delta output_prefix unique_length_required min_size max_size
Assemblytics incorporates a unique anchor filtering approach to increase robustness to repetitive elements, and identifies six classes of variants based on their distinct alignment signatures. Assemblytics can be applied both to comparing aberrant genomes, such as human cancers, to a reference, or to identify differences between related species.
Generate the delta file with nucmer(1): nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Then run the program: Assemblytics OUT.delta OUT 10000 50 10000
Maria Nattestad, Michael C. Schatz; Assemblytics: a web analytics tool for the detection of variants from an assembly, Bioinformatics, Volume 32, Issue 19, 1 October 2016, Pages 3021–3023, https://doi.org/10.1093/bioinformatics/btw369
nucmer(1), http://assemblytics.com February 11 2018 Assemblytics(1)