NAME

       MindTheGap - Perform detection and assembly of DNA insertion variants

SYNOPSIS

       MindTheGap <module> [module options]

DESCRIPTION

       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]

COMMON OPTIONS

       help - display the MindTheGap help menu
       Usage: MindTheGap -help

       version - display current version
       Usage: MindTheGap -version

                                                                                    MINDTHEGAP(1)