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Compression of next-generation sequencing reads aided by highly efficient de novo assembly
Open accessAbstract
UNLABELLED: We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based compressor, using a novel de novo assembly algorithm. A probabilistic data structure is used to dramatically reduce the memory required by traditional de Bruijn graph assemblers, allowing millions of reads to be assembled very efficiently. Read sequences are then stored as positions within the assembled contigs. This is combined with statistical compression of read identifiers, quality scores, alignment information and sequences, effectively collapsing very large data sets to <15% of their original size with no loss of information. AVAILABILITY: Quip is freely available under the 3-clause BSD license from http://cs.washington.edu/homes/dcjones/quip.
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Cites
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Wu, T. D., & Nacu, S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq057 · Cited by 1,894
Cited by
Human housekeeping genes, revisited
Eisenberg, E., & Levanon, E. Y. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.05.010 · Cited by 1,282
Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R
Wright, E. (2016) · The R Journal · doi:10.32614/rj-2016-025 · Cited by 1,016
Transcriptomics in the RNA-seq era
McGettigan, P. A. (2013) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.12.008 · Cited by 358
Lighter: fast and memory-efficient sequencing error correction without counting
Song, L., Florea, L., & Langmead, B. (2014) · Genome Biology · doi:10.1186/preaccept-9663167051308943 · Cited by 258
Metadata
- Authors
- Jones, D. C., Ruzzo, W. L., Peng, X., & Katze, M. G.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-08-13
- Volume
- 40
- Issue
- 22
- Pages
- e171-e171
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2166588423
- Cited by
- 161
- References
- 2
- FWCI
- 20.90
- Type
- journal article
- Language
- en
- Open access
- gold
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- Jones, D. C., Ruzzo, W. L., Peng, X., & Katze, M. G. (2012). Compression of next-generation sequencing reads aided by highly efficient de novo assembly. Nucleic Acids Research. https://doi.org/10.1093/nar/gks754
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