MindTheGap - Perform detection and assembly of DNA insertion variants
MindTheGap <module> [module options]
MindTheGap is designed to call insertions of any size, whether they are novel or
duplicated, homozygous or heterozygous in the donor genome. It takes as input
a set of reads and a reference genome. It outputs two sets of FASTA sequences:
one is the set of breakpoints of detected insertion sites, the other is the
set of assembled insertions for each breakpoint.
MindTheGap can also be used as a genome assembly finishing tool: it can fill the
gaps between a set of input contigs without any a priori on their relative
order and orientation. It outputs the results in gfa file.
find - insertion breakpoint detection.
Usage:
MindTheGap find ( -in
<reads.fq> | -graph
<graph.h5> ) -ref
<reference.fa> [option]
fill - gap-filler or insertion assembly
Usage:
MindTheGap fill ( -in
<reads.fq> | -graph
<graph.h5> ) ( -bkpt
<breakpoints.fa> | -contig
<contig.fa> ) [options]
help - display the MindTheGap help menu
Usage:
MindTheGap -help
version - display current version
Usage:
MindTheGap -version