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)