BFC: Correcting Illumina sequencing errors

Bioinformatics

Volumn 31, Issue 17, 2015, Pages 2885-2887

  Li, Heng ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; DNA SEQUENCE; FALSE POSITIVE RESULT; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; PROCEDURES; REPRODUCIBILITY; SOFTWARE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; FALSE POSITIVE REACTIONS; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84940767993     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv290     Document Type: Article

References (15)

1. Chaisson M., et al. (2004). Fragment assembly with short reads. Bioinformatics, 20, 2067-2074
2. Deorowicz S., et al. (2015). KMC 2: Fast, and resource-frugal k-mer counting. Bioinformatics, 31, 1569-1576
3. Drezen E., et al. (2014). GATB: Genome assembly & analysis tool box. Bioinformatics, 30, 2959-2961
4. Garrison E., and Marth G. (2012). Haplotype-based variant detection from short-read sequencing. arXiv: 1207.3907
5. Heo Y., et al. (2014). BLESS: bloom filter-based error correction solution for high-throughput sequencing reads. Bioinformatics, 30, 1354-1362
6. Li H. (2012). Exploring single-sample SNP, and INDEL calling with wholegenome de novo assembly. Bioinformatics, 28, 1838-1844
7. Li H. (2013). Aligning sequence reads, clone sequences, and assembly contigs with BWA-MEM. arXiv: 1303.3997
8. Liu Y., et al. (2013). Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics, 29, 308-315
9. Melsted P., and Pritchard J.K. (2011). Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinformatics, 12, 333
10. Pevzner P.A., et al. (2001). An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci., 98, 9748-953
11. Putze F., et al. (2007). Cache-, hash-, and space-efficient bloom filters. In: Experimental Algorithms, 6th International Workshop, WEA 2007, Rome, Italy, June 6-8, 2007, Proceedings, pp. 108-121
12. Simpson J.T., and Durbin R. (2012). Efficient de novo assembly of large genomes using compressed data structures. Genome Res., 22, 549-56
13. Simpson J.T., et al. (2009). ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123
14. Song L., et al. (2014). Lighter: fast, and memory-efficient sequencing error correction without counting. Genome Biol., 15, 509
15. Zerbino D.R., and Birney E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829