CoChat
Sign Up
Cited by 355

The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

Sherman, Rachel M., Forman, Juliet, Antonescu, Valentin, Puiu, Daniela, Daya, Michelle, Rafaels, Nicholas, Boorgula, Meher Preethi, Chavan, Sameer, Vergara, Candelaria, Ortega, Victor E., Levin, Albert M., Eng, Celeste, Yazdanbakhsh, Maria, Wilson, James G., Marrugo, Javier, Lange, Leslie A., Williams, L. Keoki, Watson, Harold, Ware, Lorraine B., Olopade, Christopher O., Olopade, Olufunmilayo, Oliveira, Ricardo R., Ober, Carole, Nicolae, Dan L., Meyers, Deborah A., Mayorga, Alvaro, Knight-Madden, Jennifer, Hartert, Tina, Hansel, Nadia N., Foreman, Marilyn G., Ford, Jean G., Faruque, Mezbah U., Dunston, Georgia M., Caraballo, Luis, Burchard, Esteban G., Bleecker, Eugene R., Araujo, Maria I., Herrera-Paz, Edwin F., Campbell, Monica, Foster, Cassandra, Taub, Margaret A., Beaty, Terri H., Ruczinski, Ingo, Mathias, Rasika A., Barnes, Kathleen C., Salzberg, Steven L.·2019·Nature Genetics
DOI 10.1038/s41588-018-0273-yPMC PMC6309586
Open this paper in CoChat — free account

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41588-018-0273-y

Cites

10 of 10 references verified0 citation errors · 0 not checkable

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.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Reference bias can take the form of unmappable reads in the presence of diverse samples or variant calls being skewed toward the reference allele.

    “This bias can take the form of unmappable reads in the presence of diverse samples 37 or, more subtly, variant calls being skewed toward the reference allele 3,6 .”

    From Pangenome graph construction from genome alignments with Minigraph-Cactus (2024) · cites this paper as [37]

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

Flagged first, then by citations

Research works printed but not linked: 26

  1. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001). · DOI · Paper page
  2. Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010). · DOI · Paper page
  3. E pluribus unum. Nat Methods 7, 331 (2010). · DOI
  4. Need, A. C. & Goldstein, D. B. Next generation disparities in human genomics: concerns and remedies. Trends Genet. 25, 489–494 (2009). · DOI · Paper page
  5. Church, D. M. et al. Extending reference assembly models. Genome. Biol. 16, 13 (2015). · DOI
  6. Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001). · DOI · Paper page
  7. Li, R. et al. Building the sequence map of the human pan-genome. Nat. Biotechnol. 28, 57–63 (2010). · DOI
  8. Seo, J. S. et al. De novo assembly and phasing of a Korean human genome. Nature 538, 243–247 (2016). · DOI
  9. Shi, L. et al. Long-read sequencing and de novo assembly of a Chinese genome. Nat. Commun. 7, 12065 (2016). · DOI
  10. Cho, Y. S. et al. An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nat. Commun. 7, 13637 (2016). · DOI
  11. Kehr, B., Melsted, P. & Halldorsson, B. V. PopIns: population-scale detection of novel sequence insertions. Bioinformatics 32, 961–967 (2016). · DOI
  12. Maretty, L. et al. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature 548, 87–91 (2017). · DOI
  13. Hehir-Kwa, J. Y. et al. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nat. Commun. 7, 12989 (2016). · DOI
  14. Kehr, B. et al. Diversity in non-repetitive human sequences not found in the reference genome. Nat. Genet. 49, 588–593 (2017). · DOI
  15. Gordienko, E. N., Kazanov, M. D. & Gelfand, M. S. Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica. J. Bacteriol. 195, 2786–2792 (2013). · DOI
  16. Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc. Natl Acad. Sci. USA 102, 13950–13955 (2005). · DOI
  17. Vernikos, G., Medini, D., Riley, D. R. & Tettelin, H. Ten years of pan-genome analyses. Curr. Opin. Microbiol. 23, 148–154 (2015). · DOI
  18. Telenti, A. et al. Deep sequencing of 10,000 human genomes. Proc. Natl Acad. Sci. USA 113, 11901–11906 (2016). · DOI
  19. Huddleston, J. et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res. 27, 677–685 (2017). · DOI
  20. Mathias, R. A. et al. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nat. Commun. 7, 12522 (2016). · DOI
  21. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009). · DOI · Paper page
  22. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012). · DOI · Paper page
  23. Zimin, A. V. et al. The MaSuRCA genome assembler. Bioinformatics 29, 2669–2677 (2013). · DOI
  24. Kim, D., Song, L., Breitwieser, F. P. & Salzberg, S. L. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 26, 1721–1729 (2016). · DOI · Paper page
  25. Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics Chapter 4, Unit 4.10, (2009). · DOI
  26. Delcher, A. L., Salzberg, S. L. & Phillippy, A. M. Using MUMmer to identify similar regions in large sequence sets. Curr. Protoc. Bioinformatics Chapter 10, Unit 10.13, (2003). · DOI

Cited by

Sorted by citations

Metadata

Authors
Sherman, R. M., Forman, J., Antonescu, V., Puiu, D., Daya, M., Rafaels, N., Boorgula, M. P., Chavan, S., Vergara, C., Ortega, V. E., Levin, A. M., Eng, C., Yazdanbakhsh, M., Wilson, J. G., Marrugo, J., Lange, L. A., Williams, L. K., Watson, H., Ware, L. B., Olopade, C. O., Olopade, O., Oliveira, R. R., Ober, C., Nicolae, D. L., Meyers, D. A., Mayorga, A., Knight-Madden, J., Hartert, T., Hansel, N. N., Foreman, M. G., Ford, J. G., Faruque, M. U., Dunston, G. M., Caraballo, L., Burchard, E. G., Bleecker, E. R., Araujo, M. I., Herrera-Paz, E. F., Campbell, M., Foster, C., Taub, M. A., Beaty, T. H., Ruczinski, I., Mathias, R. A., Barnes, K. C., & Salzberg, S. L.
ORCID
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2018-11-19
Volume
51
Issue
1
Pages
30-35
ISSN
  • 1061-4036
  • 1546-1718
DOI
10.1038/s41588-018-0273-y
PMC
PMC6309586
Cited by
355
References
10
Language
en
Update notices
correction (2019-01-15)
Licence
creativecommons.org/licenses/by/4.0 (tdm)

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