BamBam: Genome sequence analysis tools for biologists

BMC Research Notes

Volumn 7, Issue 1, 2014, Pages

  Page, Justin T ^a   Liechty, Zachary S ^a   Huynh, Mark D ^a   Udall, Joshua A ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

BAM; Consensus; Expression; Haplotype; Indel; Methylation; SAM; SNP

Indexed keywords

HYDROGEN SULFITE; SULFITE;

ALGORITHM; CLUSTER ANALYSIS; COMPUTER PROGRAM; COPY NUMBER VARIATION; DNA SEQUENCE; GENETICS; GENOME; GENOMICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES;

ALGORITHMS; BASE SEQUENCE; CLUSTER ANALYSIS; DNA COPY NUMBER VARIATIONS; GENOME; GENOMICS; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SOFTWARE; SULFITES;

EID: 84964312966     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-7-829     Document Type: Article

References (18)

1. Wu TD, Nacu S: Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 2010, 26:873-881.
2. Langmead B, Salzberg SL: Fast gapped-read alignment with bowtie 2. Nat Meth 2012, 9:357-359.
3. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J: The sequence alignment/map format and SAMtools. Oxford, UK: Bioinformatics; 2009.
4. Page JT, Gingle AR, Udall JA: PolyCat: a resource for genome categorization of sequencing reads from allopolyploid organisms. G3 (Bethesda) 2013, 3:517-525.
5. Rutkoski JE, Poland J, Jannink J-L, Sorrells ME: Imputation of unordered markers and the impact on genomic selection accuracy. G3 (Bethesda) 2013, 3:427-439.
6. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB: Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17:520-525.
7. Bansal V, Bafna V: HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. 2008.
8. Browning BL, Browning SR: A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 2009, 84:210-223.
9. He D, Eskin E: Hap-seqX: expedite algorithm for haplotype phasing with imputation using sequence data. Gene 2012, 518:2-6.
10. Lloyd S: Least squares quantization in PCM. IEEE Trans Inf Theory 1982, 28:129-137.
11. Ding C, He X: K-Means Clustering via Principal Component Analysis. New York, NY, USA: ACM Press; 2004:29.
12. Thorvaldsdóttir H, Robinson JT, Mesirov JP: Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2013, 14:178-192.
13. Zhao M, Wang Q, Wang Q, Jia P, Zhao Z: Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 2013, 14:S1.
14. Rabiner LR: A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 1989, 77:1-30.
15. Robinson MD, Robinson MD, McCarthy DJ, McCarthy DJ, Smyth GK: edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2009, 26:139-140.
16. Stajich JE, Block D, Boulez K, Brenner SE: The bioperl toolkit: Perl modules for the life sciences. Genome 2002, 12:1611-1618.
17. Barnett DW, Garrison EK, Quinlan AR: BamTools: A C++ API and Toolkit for Analyzing and Managing BAM Files. Oxford, UK: Bioinformatics; 2011.
18. Drummond AJ, Ashton B, Buxton S, Cheung M: Drummond: Geneious v5. 4-Google Scholar. Aukland, New Zealand: Biomatters Ltd; 2011.