The DOI matches its Crossref record; 138 of the 138 references it cites were found in a registry or an index.
A field guide to whole‐genome sequencing, assembly and annotation
Open accessAbstract
Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high‐throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco‐evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step‐by‐step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole‐genome sequencing projects.
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Citations
Cites
1 retracted
Evaluation of next-generation sequencing software in mapping and assembly
Bao, S., Jiang, R., Kwan, W., Wang, B., Ma, X., & Song, Y. (2011) · Journal of Human Genetics · doi:10.1038/jhg.2011.43 · Cited by 138
RetractedThe Sequence Alignment/Map format and SAMtools
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Fast and accurate short read alignment with Burrows-Wheeler transform
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KEGG: Kyoto Encyclopedia of Genes and Genomes
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Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
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BEDTools: a flexible suite of utilities for comparing genomic features
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An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
The variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,200
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Cited by
Genomics and the challenging translation into conservation practice
Shafer, A. B. A., Wolf, J. B. W., Alves, P. C., Bergström, L., Bruford, M. W., Brännström, I., Colling, G., Dalén, L., De Meester, L., Ekblom, R., et al. (2015) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2014.11.009 · Cited by 573
Self-citationPACVr: plastome assembly coverage visualization in R
Gruenstaeudl, M., & Jenke, N. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-3475-0 · Cited by 341
Conservation 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
The Value of Reference Genomes in the Conservation of Threatened Species
Brandies, P., Peel, E., Hogg, C. J., & Belov, K. (2019) · Genes · doi:10.3390/genes10110846 · Cited by 158
Technology dictates algorithms: recent developments in read alignment
Alser, M., Rotman, J., Deshpande, D., Taraszka, K., Shi, H., Baykal, P. I., Yang, H. T., Xue, V., Knyazev, S., Singer, B. D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02443-7 · Cited by 144
Metadata
- Authors
- Ekblom, R., & Wolf, J. B. W.
- Venue
- Evolutionary Applications
- Publisher
- Wiley
- Published
- 2014-06-24
- Volume
- 7
- Issue
- 9
- Pages
- 1026-1042
- ISSN
- 1752-4563 (ISSN-L)
- 1752-4571
- OpenAlex
- W1978732934
- Cited by
- 428
- References
- 138
- FWCI
- 13.51
- Type
- journal article
- Language
- en
- Open access
- gold
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