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Fei Shen edited this page Feb 8, 2023 · 35 revisions

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Welcome to the BSATOS wiki!

Author: Fei Shen PhD, China Agriculatural University Time:09/04/2018

Introduction

Bulked Segregant Analyis Tools for outbreeding species(BSATOS) is developed by the institute for horticultue plants,China Argicultural University.BSATOS is designed for NGS-based Bulked-segregant analysis for outbreeding species,includings fruits trees,such as apple,cirtus. BSATOS can also sign genotype effect value to each marker and conduct prediction using limited markers.

To improve the gene mapping efficiency of next generation sequencing-based segregant analysis (BSA) in outbreeding species and realize the rapid candidate gene mining based on multi-omics data, bulked segregant analysis tools for outbreeding species (BSATOS) was developed. Different from the classic two-way pseudo-testcross (PT) strategy, Local phased 3-way BSA mapping strategy was introduced to use three type of segregate makers unbiased. After comparing different statistical methods to evaluate the allele frequency difference, G value method was selected(Paul M. Magwene 2011). Multi-round G value screening and multi-omics data based gene mining were also integrated.

Installation

https://github.com/maypoleflyn/BSATOS/wiki/Installation

## # quick start

Let's assume that BASTOS is installed

bsatos

which will give a list of possible commands and a command line guide. All the steps of the pipeline can be manually run one after the other, but we recommend to launch the full pipeline with:

bsatos all

which will create a bash script with all the commands of the pipeline that can then be invoked to run the whole analysis process.

BSATOS will create several files and folders during its execution. See documentation (https://drive.google.com/open?id=1lUIlS3-tC181wzCqwDIqTKoz53nL9Rhm) for a description of all the files.

Demo data1 (demo_chr06)

User could download the data from FTP ftp://bsatos.top/bsatos/demo1_chr06

or download the data from baidu: link：https://pan.baidu.com/s/1oEM4Y0dFXTVLvn20eJWOmg password：0lno

input_files:

  1. reads alignment (BAM file) from two extreme pools High pool (H.bam) and Low pool (L.bam)

  2. reads alignment (BAM file) from two parents pollen parent (P.bam) and maternal parent (M.bam)

  3. genome fasta file

  4. gene.gtf file

BSATOS processes

run:

bastos all --o result --r genome.fasta --gtf gene.gtf --pb P.bam --mb M.bam --hb H.bam --lb L.bam

Demo data2 (demo2_chr10)

  1. download data from

ftp://bsatos.top/bsatos/demo2_chr10

or download from baidu link：https://pan.baidu.com/s/1az1iYtlScyslhLnRlGVK9g?pwd=534s password：534s

and you will find H.bam (pre-aligned BAM file from High pool), L.bam (pre-aligned BAM file from Low pool), M.bam (pre-aligned BAM file from maternal parent) and P.bam (pre-aligned BAM file from pollen parent).

  1. run

bastos all --o result --r genome.fasta --gtf gene.gtf --pb P.bam --mb M.bam --hb H.bam --lb L.bam

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