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The SNP Detection System


Altoros delivered an automated system for singlenucleotide polymorphism detection that provides better performance at a smaller cost.

The SNP Detection System

About the project

A common problem for researchers who work on genome analysis is the need to store and process terabytes of data fast. Deployed on Amazon public cloud, the system was powered by Amazon Web Services and Amazon EMR. With this optimal solution our customer was able to process 150 GB of genome sequencing data within 24 hours and in the most cost-efficient manner.

Apart from building an algorithm for detecting SNP, we were to determine what hardware configuration could provide the required data processing speed.

The need

The customer helps scientists and laboratories to conduct research and experiments in the field of life sciences. Their key services include next-generation sequencing, bioanalytical and mass spectrometry, as well as DNA sequencing. The customer turned to Altoros to develop a solution that would detect SNP in digitized DNA sequences saved in the FASTA/FASTQ format easier and less time-consuming.

The solution

The team completed the following tasks for this project:

  • Implementation of the data analysis algorithm. Our team designed a Web application to detect SNP and unite all tools required for genome analysis in one user-friendly interface. The software used Bowtie and SAMtools to align short DNA reads to the human genome and SOAPsnp to assemble consensus sequences and align raw sequencing reads on the known reference.
  • Assessment of computation capacities. Our customer wanted to analyze heavy sets of sequencing data with an average size of 150 GB about 2-3 times a month. All computations had to be done within a maximum of 24 hours. We deployed the system on the Amazon cloud to keep the right balance between the cost of the solution and the throughput.
  • Feasibility study and the system testing. Our team built a testing infrastructure using Amazon Web Services and Amazon Elastic MapReduce and provided a detailed report, where we indicated the cost of every solution depending on frequency of use, processing time, and amount of processed data.
  • Our customer wanted to use the OpSource cloud hosting, so Altoros developed a special module for it. When a user buys subscription, the module automatically creates the entire infrastructure. If any system errors occur, an automatic report is generated to enable manual configuration.
  • Building a private infrastructure. Although, the company was delighted with the results they achieved, they faced a new issue. The amount of data continued to grow and–eventually–they had to use AWS more frequently. It was decided to build a private infrastructure inside the customer’s laboratory.

The outcome

With the help of the automated SNP detection system, the biological laboratory of our customer managed to process 150 GB of genome sequence data within 24 hours at minimum cost. We started with development of a prototype to test the possible deployment options and make sure the functionality works correctly. The system for SNP detection was later installed on the customer’s private distributed infrastructure and data processing was performed with Apache Hadoop.

Technology stack

Server platforms

Linux, Amazon Web Services

Client Platforms/Application Servers

Internet Explorer, Firefox, Safari, Chrome

Programming languages

Perl, Java, Bash


Map / Reduce, Java, HTML, Apache Hadoop, Amazon EMR




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Ryan Meharg

Ryan Meharg

Technical Director

ryan.m@altoros.com650 265-2266

4900 Hopyard Rd. Suite 100 Pleasanton, CA 94588