SEAL
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Application data |
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| Principal bioinformatics method(s) | Read mapping |
|---|---|
| Technology | Illumina |
| Created at | CRS4 |
| Maintained? | Yes |
| Input format(s) | PRQ, QSEQ, SAM |
| Programming language(s) | Python, C++, Java |
| Licence | GPLv3 |
Summary: Read mapper and duplicate remover.
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Description
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 is part of the Biodoop suite of tools.
Seal currently contains the following tools:
- Demux - Separate sample data in the qseq file format produced by a multiplexed Illumina run.
- PairReadsQSeq - convert files in the Illumina qseq file format to prq format to be processed by the alignment program, Seqal.
- Seqal - distributed short read mapping and duplicate removal tool.
- ReadSort - distributed sorting of read mappings.
- RecabTable - distributed calculation of covariates table to estimate empirical base qualities.
Links
References
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