The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
Redundans: an assembly pipeline for highly heterozygous genomes
Open accessAbstract
Many genomes display high levels of heterozygosity (i.e. presence of different alleles at the same loci in homologous chromosomes), being those of hybrid organisms an extreme such case. The assembly of highly heterozygous genomes from short sequencing reads is a challenging task because it is difficult to accurately recover the different haplotypes. When confronted with highly heterozygous genomes, the standard assembly process tends to collapse homozygous regions and reports heterozygous regions in alternative contigs. The boundaries between homozygous and heterozygous regions result in multiple assembly paths that are hard to resolve, which leads to highly fragmented assemblies with a total size larger than expected. This, in turn, causes numerous problems in downstream analyses such as fragmented gene models, wrong gene copy number, or broken synteny. To circumvent these caveats we have developed a pipeline that specifically deals with the assembly of heterozygous genomes by introducing a step to recognise and selectively remove alternative heterozygous contigs. We tested our pipeline on simulated and naturally-occurring heterozygous genomes and compared its accuracy to other existing tools. Our method is freely available at https://github.com/Gabaldonlab/redundans.
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Cites
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
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,987
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
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
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · Gigascience · doi:10.1186/2047-217x-1-18 · Cited by 5,307
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
ABySS: A parallel assembler for short read sequence data
Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M., & Birol, İ. (2009) · Genome Research · doi:10.1101/gr.089532.108 · Cited by 3,608
Scaffolding pre-assembled contigs using SSPACE.
Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D., & Pirovano, W. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq683 · Cited by 2,337
Cited by
Identifying and removing haplotypic duplication in primary genome assemblies
Guan, D., McCarthy, S. A., Wood, J., Howe, K., Wang, Y., & Durbin, R. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa025 · Cited by 2,706
Xia, E., Tong, W., Hou, Y., An, Y., Chen, L., Wu, Q., Liu, Y., Yu, J., Li, F., Li, R., et al. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.04.010 · Cited by 452
Topological structures and syntenic conservation in sea anemone genomes
Zimmermann, B., Montenegro, J. D., Robb, S. M. C., Fropf, W. J., Weilguny, L., He, S., Chen, S., Lovegrove-Walsh, J., Hill, E. M., Chen, C.-Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-44080-7 · Cited by 106
Genomic and phenotypic evolution of nematode-infecting microsporidia
Wadi, L., El Jarkass, H. T., Tran, T. D., Islah, N., Luallen, R. J., & Reinke, A. W. (2023) · PLOS Pathogens · doi:10.1371/journal.ppat.1011510 · Cited by 32
Schikora-Tamarit, M. À., Marcet-Houben, M., Nosek, J., & Gabaldón, T. (2021) · Open Biology · doi:10.1098/rsob.200362 · Cited by 16
Self-citation
Metadata
- Authors
- Pryszcz, L. P., & Gabaldón, T.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-04-29
- Volume
- 44
- Issue
- 12
- Pages
- e113-e113
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2344852138
- Cited by
- 522
- References
- 27
- FWCI
- 15.50
- Type
- journal article
- Language
- en
- Open access
- gold
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