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Get Seal


Seal is developed by: crs4 logo

And generously hosted by Get SEAL at Fast, secure and Free Open Source software downloads
and GitHub


Seal is a suite of distributed applications for aligning short DNA reads, and manipulating and analyzing short read alignments. Seal applications generally run on the Hadoop framework and are made to scale well in the amount of computing nodes available and the amount of the data to process. This fact makes Seal particularly well suited for processing large data sets.


Seal currently contains the following Hadoop-based tools.

Extract reads in qseq format from an Illumina run directory.
Separate sample data in the qseq file format produced by a multiplexed Illumina run.
convert files in the Illumina qseq file format to prq format to be processed by the alignment program, Seqal.
Distributed short read mapping and duplicate removal tool.
Distributed sorting of read mappings.
distributed calculation of covariates table to estimate empirical base qualities.

Please see each individual tool’s page for specific details.

Do you need Seal?

Seal has been built with large data sets in mind, like those produced by whole genome sequencing runs. If you’re aligning read datasets of more than a couple of hundred MB, and you have a cluster of computers (even a small one, say 4 or 5 nodes, and up to hundreds of nodes) then Seal might be for you.

Seal provides a number of important features.

Scalability and speed

Seal can efficiently use the computer power of a large number of nodes. We have successfully tested SEAL of 500GB datasets, running on 16- to 128-node clusters. Thanks to its ability to scale, Seal can achieve very high throughputs by harnessing the computing power of many machines. And when you need more speed, you can simply add more machines.

Memory efficiency

Seal can use your computer’s resources more efficiently than other alignment tools. Thanks to its use of shared memory, as many as 7 or 8 alignment processes can be run concurrently on a single workstation with 8 GB of memory, using a Human reference genome (UCSC HG18, for instance).


Thanks to Hadoop, Seal provides a start-and-forget solution, resisting node failures and transient cluster conditions that may cause your jobs to fail. It also avoids basing all operations on a centralized shared stored volume, which can represent a single point of failure.


Seal is currently used to process all the DNA sequenced at the CRS4 Sequencing and Genotyping Platform.