asmkit

README

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

Documentation

Index

• Constants
• func Execute() error
• type AGP
  • func (r *AGP) Add(row string)
• type AGPLine
• type Agp2assembler
  • func (r *Agp2assembler) AGP2Assembly() error
  • func (r *Agp2assembler) Run() error
• type Bam2linker
  • func (r *Bam2linker) ExtractLinks() error
  • func (r *Bam2linker) Run() error
• type BamStater
  • func (r *BamStater) BamStat() error
  • func (r *BamStater) Run() error
• type LinkLine

Constants

const (
	Version = "0.0.2"
	Author  = "Yibin Wang"
	License = "BSD 3-Clause"
)

Functions

func Execute

func Execute() error

Types

type AGP

type AGP struct {
	// contains filtered or unexported fields
}

AGP is a collection of AGPLines

func (*AGP) Add

func (r *AGP) Add(row string)

Add adds an AGPLine to the collection from github.com/tanghaibao/allhic

type AGPLine

type AGPLine struct {
	// contains filtered or unexported fields
}

AGPLine github.com/tanghaibao/allhic

type Agp2assembler

type Agp2assembler struct {
	Agpfile      string
	Assemblyfile string
}

Agp2assembler

func (*Agp2assembler) AGP2Assembly

func (r *Agp2assembler) AGP2Assembly() error

func (*Agp2assembler) Run

func (r *Agp2assembler) Run() error

type Bam2linker

type Bam2linker struct {
	Bamfile  string
	Linkfile string
}

Bam2linker

func (*Bam2linker) ExtractLinks

func (r *Bam2linker) ExtractLinks() error

func (*Bam2linker) Run

func (r *Bam2linker) Run() error

type BamStater

type BamStater struct {
	Bamfile string
	MapQ    int
}

func (*BamStater) BamStat

func (r *BamStater) BamStat() error

func (*BamStater) Run

func (r *BamStater) Run() error

type LinkLine

type LinkLine struct {
	// contains filtered or unexported fields
}

LinkLine stores link information