.TH Assemblytics 1 "February 11 2018"
.\" Please adjust this date whenever revising the manpage.
.\"
.\" Some roff macros, for reference:
.\" .nh        disable hyphenation
.\" .hy        enable hyphenation
.\" .ad l      left justify
.\" .ad b      justify to both left and right margins
.\" .nf        disable filling
.\" .fi        enable filling
.\" .br        insert line break
.\" .sp <n>    insert n+1 empty lines
.\" for manpage-specific macros, see man(7)
.SH NAME
Assemblytics \- detect and analyze structural variants from a genome assembly
.SH SYNOPSIS
.B Assemblytics
.I delta output_prefix unique_length_required min_size max_size
.SH DESCRIPTION
.B 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.
.B Assemblytics
can be applied both to comparing aberrant genomes, such as human cancers, to a reference, or to identify differences between related species.
.SH EXAMPLES
Generate the delta file with
.BR nucmer (1):

.RS 4
nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT
.RE
.sp 1
Then run the program:

.RS 4
Assemblytics OUT.delta OUT 10000 50 10000
.RE
.SH 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
.SH SEE ALSO
.BR nucmer (1),
http://assemblytics.com