Quip
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Application data |
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| Created by | Daniel C. Jones |
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| Principal bioinformatics method(s) | File reformatting |
| Created at | University of Washington |
| Maintained? | Yes |
| Input format(s) | FASTQ, SAM, BAM |
| Output format(s) | Quip |
| Programming language(s) | C |
| Licence | BSD (3-clause) |
| Operating system(s) | any |
Summary: Aggressive compression of FASTQ and SAM/BAM files.
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Description
Quip implements an ensemble of compression techniques specially built to compress sequencing reads as much as possible. The basis of the algorithm is statistical compression of read identifiers, quality scores, and nucleotide sequences using arithmetic coding. In addition, we implement reference-based compression in which aligned reads are stored a positions within a genome. And, when no reference genome is available, an extremely efficient de novo assembly algorithm can transparently construct one.
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References
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