Manigben / IBSA

software for BSA-seq based on PyQt

IBSA

introduction

An Integrated GUI software for BSA-seq based on PyQt. Users can use the software to analyze and draw the VCF file. The software provides MutMap, QTL-Seq,Modified Mutmap, Grade Pool-seq,Fihser-seq.It also provides a mapping function of genome circle map. Users only need to install it to work, set parameters, and download the required pictures and tables.

installtion

Dependencies

• sys
• PyQt5
• pandas
• numpy
• re
• matplotlib
• scipy
• math

download package

down code

Useage

Input file

a VCF include all sample you need,and include the variant you need.If you only focus on SNPs,use the file only include SNPs. if you install manually, python IBSA.py We provide these method.

method	bulk	index	threshold
Mutmap	1-2 parent,1 bulk	SNP-index	-
QTL-seq	1-2 parent,2 bulk	SNP-index,delta SNP-index,ED6	p99
Modified Mutmap	2bulk	delta SNP-index,ED6	p99
Fisher	2 bulk	-log10(p) (Fisher's exact test)	3
Graded Pool-seq	0-2 parent,>1 bulk	-log10(p) (Ridit)	the highest p window

1.uplod file and choose method

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2.setting

setting sample names,if you use Grade-Pool seq,please input bulk name,split by comma.firstly,click first 'NEXT' button,caculate index based on samples. Then setting slide window paremters and click second 'NEXT' button to smooth the index.

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3.plotting

Tab to another page then click 'plotting' button,the picture will show.

4.downlod

Click the corresponding button to download the file.