https://github.com/LeilyR/Multi-genome-Reference

A program to generate a graph which presents a simplified representation of several full length genomes
https://github.com/LeilyR/Multi-genome-Reference

Last synced: 8 days ago
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A program to generate a graph which presents a simplified representation of several full length genomes

• Host: GitHub
• URL: https://github.com/LeilyR/Multi-genome-Reference
• Owner: LeilyR
• Created: 2018-06-28T08:54:21.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2018-08-23T06:41:17.000Z (over 6 years ago)
• Last Synced: 2023-10-20T21:12:54.376Z (about 1 year ago)
• Language: C++
• Size: 16.6 MB
• Stars: 12
• Watchers: 0
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-pangenomes - MGRgraph - genome Reference (warning - last updated 2018) (A list of software capable of analyzing mainly **eukaryotic** genomes for pangenomics. A new section for microbial genomes has also been added, these tools may not scale to large genomes.)

README

        
This program generates a genome graph

1. To compile the program:

	i. Go to the src directory

	ii.make

2. Change the library path to the 'src' directory

	export LD_LIBRARY_PATH= [...]/src

3. Input Fasta file should be changed to the foramt is acceptable by the program run:

	../src/graph fasta_prepare prepared_fasta input1_fasta input2_fasta [...] inputn_fasta

4. Use the prepared_fasta to generate a maf file contains pairwise alignments

	Any aligner can be used 

5. After having the input_maf file, to built the graph run:

	../src/graph build_graph prepared_fasta input_maf output_maf output_encode(noencode) output_fasta ourput_dot output_gfa(nogfa) output_txt 0(1) number_of_threads(optional)

	

	0: generate graphs with longer nodes

	1: generate graphs with shorter nodes

	noencode: if don't need the arithmetically encoded output file

	nogfa: if dont' need the gfa output file

6. To decode the output_encode 

	../src/graph dy_decoding output_encode 0(1) output_decode

	

	0 or 1 determine the center type which was used in buildign the graph.