Assemblytics1
Detect and analyze structural variants from a genome assembly
Usage
Assemblytics delta
output_prefix
unique_length_required
min_size
max_size
Overview
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.
Examples
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
Citation
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
Releases
Unchanged in 2 releases since Debian 10 (Buster).