The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Stacks: an analysis tool set for population genomics
Open accessAbstract
Massively parallel short‐read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of theS tacks software package to efficiently use genotype‐by‐sequencing data for studies of populations of organisms.Stacks now produces core population genomic summary statistics and SNP‐by‐SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window.Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions inS tacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
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Cites
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
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
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
The hitch-hiking effect of a favourable gene
Smith, J. M., & Haigh, J. (1974) · Genetical Research · doi:10.1017/s0016672300014634 · Cited by 3,415
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
Kofler, R., Pandey, R. V., & Schlötterer, C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr589 · Cited by 815
Cited by
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A., Qiu, Y., et al. (2021) · Science · doi:10.1126/science.abg5289 · Cited by 747
Linck, E., & Battey, C. J. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.12995 · Cited by 394
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-citationConservation and the Genomics of Populations
Allendorf, F. W., Funk, W. C., Aitken, S. N., Byrne, M., Luikart, G., & Antunes, A. (2022) · doi:10.1093/oso/9780198856566.001.0001 · Cited by 207
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
Metadata
- Authors
- Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A.
- Venue
- Molecular Ecology
- Publisher
- Wiley
- Published
- 2013-05-24
- Volume
- 22
- Issue
- 11
- Pages
- 3124-3140
- ISSN
- 0962-1083 (ISSN-L)
- 1365-294X
- OpenAlex
- W2108524369
- Cited by
- 4,005
- References
- 6
- FWCI
- 71.42
- Type
- journal article
- Language
- en
- Open access
- green
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