The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
Open accessAbstract
Advances in sequencing technology provide special opportunities for genotyping individuals with speed and thrift, but the lack of software to automate the calling of tens of thousands of genotypes over hundreds of individuals has hindered progress. Stacks is a software system that uses short-read sequence data to identify and genotype loci in a set of individuals either de novo or by comparison to a reference genome. From reduced representation Illumina sequence data, such as RAD-tags, Stacks can recover thousands of single nucleotide polymorphism (SNP) markers useful for the genetic analysis of crosses or populations. Stacks can generate markers for ultra-dense genetic linkage maps, facilitate the examination of population phylogeography, and help in reference genome assembly. We report here the algorithms implemented in Stacks and demonstrate their efficacy by constructing loci from simulated RAD-tags taken from the stickleback reference genome and by recapitulating and improving a genetic map of the zebrafish, Danio rerio.
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
SEGREGATION ANALYSES AND GENE-CENTROMERE DISTANCES IN ZEBRAFISH
Streisinger, G., Singer, F., Walker, C., Knauber, D., & Dower, N. (1986) · Genetics · doi:10.1093/genetics/112.2.311 · Cited by 245
Cited by
Lu, F., Lipka, A. E., Glaubitz, J., Elshire, R., Cherney, J. H., Casler, M. D., Buckler, E. S., & Costich, D. E. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003215 · Cited by 659
Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains
Wilson, C. A., High, S. K., McCluskey, B. M., Amores, A., Yan, Y.-L., Titus, T. A., Anderson, J. L., Batzel, P., Carvan, M. J., Schartl, M., et al. (2014) · Genetics · doi:10.1534/genetics.114.169284 · Cited by 331
Self-citationThe sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications
Smith, J. J., & Keinath, M. C. (2015) · Genome Research · doi:10.1101/gr.184135.114 · Cited by 152
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Stankowski, S., Chase, M. A., Fuiten, A. M., Rodrigues, M. F., Ralph, P. L., & Streisfeld, M. A. (2019) · PLOS Biology · doi:10.1371/journal.pbio.3000391 · Cited by 134
A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo.
Braasch, I., Peterson, S. M., Desvignes, T., McCluskey, B. M., Batzel, P., & Postlethwait, J. H. (2015) · Journal of Experimental Zoology Part B: Molecular and Developmental Evolution · doi:10.1002/jez.b.22589 · Cited by 122
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Metadata
- Authors
- Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W., & Postlethwait, J. H.
- Venue
- G3 Genes|Genomes|Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-08-01
- Volume
- 1
- Issue
- 3
- Pages
- 171-182
- ISSN
- 2160-1836 (ISSN-L)
- OpenAlex
- W2161901637
- Cited by
- 1,932
- References
- 6
- FWCI
- 19.63
- Type
- journal article
- Language
- en
- Open access
- gold
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