iDentification of pIG breeds (iDIGs)

iDIGs v1.0 includes a SNP dataset of a wide range of pig breeds. The dataset are used for pig breed idetification and panel design. See How to for detail functions.

Reference Samples Distribution

3605 samples

Genome-wide information were used

124 pig breeds

Covering main pig breeds across the world

45 sites

Samples were distributed in 45 sites of 24 countries

PLS distribution of all samples

All sample info

All breed info

Breed Identification analysis

First step: Data upload


Second step: Choose reference breeds (Optional)


Third step: E-mail address and submit

Design a small panel for breed identification of some specfic breeds

First step: Select panel density


Second step: Choose reference breeds

Third step: E-mail address and submit

Introduction

Welcome to iDentification of pIG breeds (iDIGs) v1.0 !

iDIGs is a tool for global pig breed identification. Our database has 3,622 samples and 124 breeds worldwide. Now, iDIGs has two mian functions: pig breed identification and panel design for specific breeds identification.

  1. Breed Identification
  2. Panel Design
Function

1. Breed Identification

Using our database to recognize users' pig breed

  • Step1: Choose the version of your reference pig genome (10.2 or 11.1) and upload your PLINK binary file. No missing SNPs are allowed . You can perform imputation using PHARP or Beagle.
  • Step2: Choose reference breeds ( Optional ). If not chose, all breeds in our database will be used as reference.
  • Step3: Input your E-mail address and submit. The results will send to the E-mail address automatically.
  • Results: A table of two columns. The first column is the input sampleID. The second column is the putative breed label.

2. Panel Design

Designing a small panel to distinguish some specific breeds from each other.

  • Step1: Choose the version of your reference pig genome (10.2 or 11.1) and the SNP number in the panel. Note that, the SNP number should be less than 10,000.
  • Step2: choose breeds you want to distinguish from. You can input multiple breed IDs or a single breed ID. If you input multiple breed IDs, markers that can distinguish all input breeds from each other will be selected. If you input a single breed ID, Markers that can distinguish your input breed from all other breeds in our database will be selected.
  • Step3: Input your E-mail address and submit. The results will send to the E-mail address automatically.
  • Results: 1) marker ID used in panel and 2) performance estimation of the panel using 5-fold CV. The preformance can be imporved by increasing the SNP number.
FAQ

Q: What type of data may i uploaded when using iDIGs?

A: We recommand commercial SNP Chips and WGS.

Q: How could i upload big PLINK binary files, such as SNPs from WGS data?

A: Big data (file size > 1 GB), such as WGS data, is hardly upload. Thus, you can download our markerID and only extract overlapped markers to upload. 

# if using LINUX
chmod +x MakeSNPidL
# Normalize your markerID and copy files
MakeSNPidL file.bim file.tmp.bim
cp file.bed file.tmp.bed
cp file.fam file.tmp.fam
# extract overlapped SNPs
plink --bfile file.tmp --extract MarkerID_11.txt --make-bed --out upload
Contact

Any questions, bug reports and suggestions can be posted to E-mail:

zhe_zhang@zju.edu.cn or miaojian6363@163.com

Hints

This software is intended for academic use only and not for commercial use. We are not legally responsible for any unauthorized commercial application.