MINDTHEGAP(1)

Okay bestie, welcome to MINDTHEGAP(1), the general commands manual page for the tool that's literally all about insertions and gaps 💖 Let's get into it ✨

🌸 NAME 🌸

MindTheGap — perform detection and assembly of DNA insertion variants 🧬

🎀 SYNOPSIS 🎀

MindTheGap <module> [module options]

💖 DESCRIPTION 💖

Okay so MindTheGap is giving insertion detective energy 🔍 It can call insertions of any size, whether they're novel or duplicated, and whether they're homozygous or heterozygous in the donor genome. You feed it a set of reads and a reference genome, and it spits out two sets of FASTA sequences. One is the breakpoints of the detected insertion sites, and the other is the assembled insertion for each breakpoint. Iconic, honestly 👑

It also doubles 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, so it doesn't need you to already know how they go together. The results come out in a gfa file 🦋

MindTheGap has two modules that do the main work:

🔍 find

Insertion breakpoint detection, the module that finds where the insertions are 💅

MindTheGap find ( -in <reads.fq> | -graph <graph.h5> ) -ref <reference.fa> [option]

🧩 fill

Gap-filler or insertion assembly, the module that fills in the blanks ✨

MindTheGap fill ( -in <reads.fq> | -graph <graph.h5> ) ( -bkpt <breakpoints.fa> | -contig <contig.fa> ) [options]

🌈 COMMON OPTIONS 🌈

These ones work across the whole thing, no cap 🫶

🙋 help

Pulls up the MindTheGap help menu, so you can check the vibes anytime 💜 Usage:

MindTheGap -help

🔢 version

Shows you the current version of MindTheGap ⭐ Usage:

MindTheGap -version

And that's a wrap on MINDTHEGAP(1) 💖 Go find those gaps and slay the assembly, bestie 🦋💅