alexcorm/boss

A new algorithm for scaffolding

BOSS(Building Optimized Scaffold graph for Scaffolding)

A novel algorithm is used for scaffolding contigs produced by any assembler.

License

Copyright (C) 2014 Jianxin Wang([email protected]), Junwei Luo([email protected])

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, see http://www.gnu.org/licenses/.

Jianxin Wang([email protected]), Junwei Luo([email protected]) School of Information Science and Engineering Central South University ChangSha CHINA, 410083

Scaffolder: BOSS

1. Introduction

   BOSS is an scaffolder which aims to determine the orientations and orders of contigs. The contigs can be produced by any assembler. The input read data of BOSS is paired-end or Mate-pair read set, in which the left read library and the right read library should have the same read length.

2. Before installing and running

	First, Please build and install bamtools from https://github.com/pezmaster31/bamtools. 
	
	And add enviroment vairable "BAMTOOLS_HOME_INCLUDE" which is the path that includes two 
	directories "api" and "shared" of bamtools. And add enviroment vairable "BAMTOOLS_HOME_LIB" 
	which is the path that includes the file "libbamtools.a".
	
	Before scaffolding, users should use one mapping tool to map left read library and right read libray to contigs.
	BOSS needs the bam files as input file, which can be produced by following commands:
	
	(a) Mapping tool: Bowtie2
	./bowtie2-build contigs.fa contigs
	./bowtie2 -x contigs left.fastq -S left.sam
	./bowtie2 -x contigs right.fastq -S right.sam
	./samtools view -Sb left.sam > left.bam
	./samtools view -Sb right.sam > right.bam
	
	(b) Mapping tool: Bowtie
	./bowtie-build contigs.fa contigs
	./bowtie -v 3 -q contigs left.fastq -S left.sam (or ./bowtie -v 0 -q contigs left.fastq -S left.sam)
	./bowtie -v 3 -q contigs right.fastq -S right.sam (or ./bowtie -v 0 -q contigs right.fastq -S right.sam)
	./samtools view -Sb left.sam > left.bam
	./samtools view -Sb right.sam > right.bam
	
	(c) Mapping tool: BWA
	./bwa index contigs.fa
	./bwa mem contigs.fa left.fastq > left.sam
	./bwa mem contigs.fa right.fastq > right.sam
	./samtools view -Sb left.sam > left.bam
	./samtools view -Sb right.sam > right.bam

3. Installing.

	BOSS should run on Linux operating sysetm with gcc. We test BOSS using gcc4.6.3 on Ubuntu.
	Create a main directory (eg:BOSS). Copy all source code to this directory.
	cd BOSS
	make all

4. Running.

	Run command line: 
	"boss <contigs.fa> <bamfile_left.bam> <bamfile_right.bam> <read_length> <insert_size> <std> <min_weight> <min_number> <is_paired_end> <edge_weight_method> <scaffold_file_name>"
	<contigs.fa>: 
		The file includes contigs produced by one assembler.
	<bamfile_left.bam>:
		Before scaffolding, users should using one mapping tool(bowtie2, bwa or bowtie) to map left read library to contigs, and this will produce the bamfile_left.bam.
	<bamfile_right.bam>:
		Before scaffolding, users should using one mapping tool(bowtie2, bwa or bowtie) to map right read library to contigs, and this will produce the bamfile_right.bam.
	<read_length>: 
		The length of read.
	<insert_size>: 
		The insert size of read library.
	<std_percentage>: 
		The percentage of standard deviation to insert size, std = insert_size*std_percentage. In default, std_percentage = 0.07.
	<min_weight>: 
		One cutoff for removing suprious edgs in the scaffold graph. In default, min_weight = 0.2. If the coverage is larger than 100, the value of min_weight can set to be 0.3 or more large. Note that, min_weight is smaller than 1.
	<min_number>: 
		The minimum number of links between contigs. In default, min_number = 2. If the coverage is larger than 100, the value of min_number can set to be 3 or more large.
	<is_paired_end>: 
		It is equal to 0 or 1, 1 represents that read library is paired-end library, 0 represents that read library is mate-paired library.
	<edge_weight_method>: 
		It is equal to 0 or 1, 0 represents that the edge weight calculated by arithmetic mean, 1 represents that the edge weight calculated by geometric mean.
	<scaffold_file_name>: 
		The output file name, this file includes scaffolds produced by BOSS. 

5. Example:

	(a). If there is one read library:
	./boss contigs.fa left.bam right.bam 76 650 0.07 0.2 2 0 0 result
	This command will produce the scaffolding result: result_ScaffoldSet.fa
	
	(b). If there are two read libraries:
	./boss contigs.fa left1.bam right1.bam 76 650 0.07 0.2 2 0 0 left2.bam right2.bam 75 2700 0.07 0.2 2 0 0 result_com
	This command will produce the scaffolding result: result_com_ScaffoldSet.fa

6）Suggestion:

When you want to enhance the accuracy of scaffolding results, please set large numbers for the parameters  <min_weight> and <min_number>;
When the coverage number of paired read library is small (smaller than 30), you can try small numbers for the parameters <min_weight> and <min_number>;   

7) Evaluation:
	You can use the tool  QUAST (http://bioinf.spbau.ru/quast) or GAGE (in the directory GAGE) to evaluate results.