Neomachine
Variant calling tools suite
Help section
Thank you for your interest in Neomachine. Our goal is to develop easy to use variant tools suite that can be used by biologists and folks
without a ton of bioinformatics knowledge. Below you will see three tools for variant analysis, and these are continually being
updated to add new features and enhance functionality.
You can use the test file linked here to see how the tool works Test file
Single sample(germline)
This tool enables one to identify disease causing germline variants. It accepts input as a single unannotated vcf. Upload the variants file
Sample results
New Antigen analysis
This tool accepts vcf input in the form somatic variant calls. Upload the vcf file using the upload button.
It assumes GRCH38 assembly, unless user selects assembly GRCh37.The tool annotates the vcf to identify
missense variants using SnpEFF. Once, missense variants have been identified, mutated peptides are generated.
These peptides are then used to identify binding affinities using NetMHC-4.0 Once the form is submitted,
it opens a window that shows the status of the job. Copy the link and refresh the page to check its status. Once the job is finished, it generates a result link like below,
generated from a sample file Test Results
Coming Soon
Compare the binding affinity with the reference peptides and identify most optimal new antigen
Thank you for your interest in Neomachine. Our goal is to develop easy to use variant tools suite that can be used by biologists and folks
without a ton of bioinformatics knowledge. Below you will see three tools for variant analysis, and these are continually being
updated to add new features and enhance functionality.
| OS | Version | Chrome | Firefox | Microsoft Edge | Safari |
|---|---|---|---|---|---|
| MacOS | Catalina v10.15.7 | Version 87.0.4280.88 | 82.0.3 (64-bit) | N/A | Version 14.0.1 |
| Windows | Catalina v10.15.7 | not tested | not tested | N/A | N/A |
| Linux | not tested | not tested | not tested | N/A | N/A |
You can use the test file linked here to see how the tool works Test file
Single sample(germline)
This tool enables one to identify disease causing germline variants. It accepts input as a single unannotated vcf. Upload the variants file
Sample results
New Antigen analysis
This tool accepts vcf input in the form somatic variant calls. Upload the vcf file using the upload button.
It assumes GRCH38 assembly, unless user selects assembly GRCh37.The tool annotates the vcf to identify
missense variants using SnpEFF. Once, missense variants have been identified, mutated peptides are generated.
These peptides are then used to identify binding affinities using NetMHC-4.0 Once the form is submitted,
it opens a window that shows the status of the job. Copy the link and refresh the page to check its status. Once the job is finished, it generates a result link like below,
generated from a sample file Test Results
Coming Soon
Compare the binding affinity with the reference peptides and identify most optimal new antigen