News ADGAP: a user-friendly online Ancient DNA Database and Genome Analysis Platform

[Tautalus]

This paper presents ADGAP, an online Ancient DNA Database and Genome Analysis Platform designed to improve accessibility and usability of ancient genomic datasets. Traditional resources like the Allen Ancient DNA Resource (AADR) and AdmixTools require advanced computational skills, limiting accessibility for many researchers. ADGAP was developed to provide a user-friendly interface for ancient DNA research, allowing researchers with limited programming expertise to analyze data more easily. The platform consists of an AADR-based resource browsing and visualization that allows researchers to browse ancient DNA databases, filter data, and visualize allele frequency distributions on an interactive map with a timeline feature. There are population genetics analysis tools, it Includes six analytical tools such as PCA, ADMIXTURE, f3-statistics, f4-statistics, qpWave, and qpAdm. ADGAP enables secure upload and analysis of genotype data. User data is encrypted and temporarily stored, with all data and results automatically deleted after two weeks to ensure privacy. The platform enables analysis of genetic adaptations (for example, lactase persistence, high-altitude adaptation) and provides insights into population migration patterns and evolutionary changes. It as a user-friendly interface, its interactive visualization tools allow to dynamically explore results. This platform was designed to facilitate the study of ancient DNA, making complex genomic analysis more accessible.
ADGAP uses EIGENSTRAT/PACKEDANCESTYMAP format as the standard input for genotype data.
Creating an account is necessary to use the available tools.

ADGAP: a user-friendly online Ancient DNA Database and Genome Analysis Platform​

ADGAP

adgap.online

Overview of the ADGAP online genomic analysis function.

 

[Thucydides enjoyer]

This paper presents ADGAP, an online Ancient DNA Database and Genome Analysis Platform designed to improve accessibility and usability of ancient genomic datasets. Traditional resources like the Allen Ancient DNA Resource (AADR) and AdmixTools require advanced computational skills, limiting accessibility for many researchers. ADGAP was developed to provide a user-friendly interface for ancient DNA research, allowing researchers with limited programming expertise to analyze data more easily. The platform consists of an AADR-based resource browsing and visualization that allows researchers to browse ancient DNA databases, filter data, and visualize allele frequency distributions on an interactive map with a timeline feature. There are population genetics analysis tools, it Includes six analytical tools such as PCA, ADMIXTURE, f3-statistics, f4-statistics, qpWave, and qpAdm. ADGAP enables secure upload and analysis of genotype data. User data is encrypted and temporarily stored, with all data and results automatically deleted after two weeks to ensure privacy. The platform enables analysis of genetic adaptations (for example, lactase persistence, high-altitude adaptation) and provides insights into population migration patterns and evolutionary changes. It as a user-friendly interface, its interactive visualization tools allow to dynamically explore results. This platform was designed to facilitate the study of ancient DNA, making complex genomic analysis more accessible.
ADGAP uses EIGENSTRAT/PACKEDANCESTYMAP format as the standard input for genotype data.
Creating an account is necessary to use the available tools.

ADGAP: a user-friendly online Ancient DNA Database and Genome Analysis Platform​

Overview of the ADGAP online genomic analysis function.

where can we download the ancient samples data tho?Because as you stated it requires the eigenstrat format.

 

[Tautalus]

The ancient samples data can be downloaded here :
Allen Ancient DNA Resource (AADR)

ADGAP has a data extractor that can extract subsets from EIGENSTRAT and PACKEDANCESTRYMAP datasets based on population lists. It can be downloaded here.

Screenshot from the Data Extractor

You can download a demo data from ADGAP, for example, here (account needed).

 

[Thucydides enjoyer]

When it says failure,the model fails,or smth went wrong?

 

[Tautalus]

When it says failure,the model fails,or smth went wrong?

It's not clear why it might have occurred and there is no feedback or documentation that can be consulted on the subject. The model has probably failed.

 

[Thucydides enjoyer]

View attachment 18310
When it says failure,the model fails,or smth went wrong?

It's not clear why it might have occurred and there is no feedback or documentation that can be consulted on the subject. The model has probably failed.

I was trying to use ancient balkan and mena population(+central asian and eastern european) with modern pops of the area,but when i try to run an admixture analysis the model instantly failes.Maybe I shouldnt use modern together with ancient pops?Is there a problem with my pop-list?

(btw i have already extracted these in the extraction tool of the website,although it shows me an error,although it must not be anything,because later i can succesfully submit the files in data preparation)