NAME

       Assemblytics - detect and analyze structural variants from a genome assembly

SYNOPSIS

       Assemblytics delta output_prefix unique_length_required min_size max_size

DESCRIPTION

       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

SEE ALSO

       nucmer(1), http://assemblytics.com

                                         February 11 2018                         Assemblytics(1)