asmkit

Toolkit for genome assembly

Introduction

asmkit provide some useful tools for genome scaffolding, especially design for ALLHiC.

Installation

The easiest way to install asmkit is to download the latest binary from the releases

Build from source with:

go get -u -t -v github.com/wangyibin/asmkit/...
go install github.com/wangyibin/asmkit

Usage

agp2assembly

asmkit agp2assembly input.agp output.assembly

bam2links

asmkit bam2links input.bam output.links

Example

From bam to juicebox assembly tool

Depend on 3D-DNA, please first downloand it.

asmkit agp2assembly sample.agp sample.assembly
asmkit bam2links sample.bwa_mem.bam sample.links
bash ~/software/3d-dna/visualize/run-assembly-visualizer.sh sample.assembly sample.links

And then import sample.hic and sample.assembly into juicebox to manual curate genome assembly