Goby framework
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Application data |
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| Created by | Campagne F, Andrews S, Deng X |
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| Biological application domain(s) | RNA-Seq |
| Principal bioinformatics method(s) | File reformatting |
| Technology | Illumina, ABI SOLiD, 454 |
| Created at | Weill Medical College, Cornell University |
| Maintained? | Yes |
| Programming language(s) | Java |
| Licence | GPLv2 |
Summary: Goby is a next-gen data management framework designed to facilitate the implementation of efficient next-gen data analysis pipelines.
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Goby provides compressed file formats that are time and space efficient. It also provides a few utilities, built on top of the Goby Java API, that support the most common secondary data analyses. Goby defines and uses several file formats. These formats include:
- compact reads An alternative to FASTA/FASTQ, which is fast to parse, unambiguous, compact, and chunckable. Chunkability means that a very large file can be processed in independent chunks without having to traverse the entire file, just the chunk of interest can be read. This property is leveraged by GobyWeb to support parallel alignments.
- compact alignments An alternative to Elan text format, MAQ, or SAM. Goby alignments are chunkable, compact, unambiuous, fast to parse.
- counts A representation of the histogram of read count along a reference sequence, at single base pair resolution. This representation is highly space efficient. Each count transition (positions where the value of the count changes along the histogram) is generally encoded in about 13 bits.
- count archives An archive of counts, one histogram per reference sequence in an alignment. Archives can store histogram data for a complete genome. They are very space efficient, with only about 20Mb needed to store a histogram of reads aligned against the human genome at base pair resolution. In contrast, a wiggle plot stored at 20bp resolution needs about 45Mb.
In addition to these file formats, Goby provides utilities that implement common next-gen data computations. See the Goby Wiki for details.
References
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