The DOI matches its Crossref record; 56 of the 56 references it cites were found in a registry or an index.
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies
Open accessAbstract
Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
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
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,304
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
Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971
Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., et al. (1996) · Science · doi:10.1126/science.274.5287.546 · Cited by 4,263
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., et al. (2009) · Science · doi:10.1126/science.1178534 · Cited by 4,046
Cited by
Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
Qin, P., Lu, H., Du, H., Wang, H., Chen, W., Chen, Z., He, Q., Ou, S., Zhang, H., Li, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.046 · Cited by 578
Massive haplotypes underlie ecotypic differentiation in sunflowers
Todesco, M., Owens, G. L., Bercovich, N., Légaré, J.-S., Soudi, S., Burge, D. O., Huang, K., Ostevik, K. L., Drummond, E. B. M., Imerovski, I., et al. (2020) · Nature · doi:10.1038/s41586-020-2467-6 · Cited by 513
Chen, Z. J., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L. M., Hulse-Kemp, A. M., Ding, M., Ye, W., Kirkbride, R. C., Jenkins, J., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0614-5 · Cited by 462
Genome evolution and diversity of wild and cultivated potatoes
Tang, D., Jia, Y., Zhang, J., Li, H., Cheng, L., Wang, P., Bao, Z., Liu, Z., Feng, S., Zhu, X., et al. (2022) · Nature · doi:10.1038/s41586-022-04822-x · Cited by 367
Semi-automated assembly of high-quality diploid human reference genomes
Jarvis, E. D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M. R., Porubsky, D., et al. (2022) · Nature · doi:10.1038/s41586-022-05325-5 · Cited by 209
Metadata
- Authors
- Goel, M., Sun, H., Jiao, W.-B., & Schneeberger, K.
- Venue
- Genome Biology
- Published
- 2019-12
- Volume
- 20
- Issue
- 1
- Pages
- 277-277
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2994888090
- Cited by
- 1,045
- References
- 56
- FWCI
- 25.06
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. https://app.cochat.ai/papers/10.1186/s13059-019-1911-0
- The paper
- Goel, M., Sun, H., Jiao, W.-B., & Schneeberger, K. (2019). SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biology. https://doi.org/10.1186/s13059-019-1911-0
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
