The DOI matches its OpenAlex record; 18 of the 18 references it cites were found in a registry or an index.
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Open accessAbstract
Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.
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
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
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
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
Self-citationMauve: Multiple alignment of conserved genomic sequence with rearrangements
Darling, A. C. E., Mau, B., Blattner, F. R., & Perna, N. T. (2004) · Genome Research · doi:10.1101/gr.2289704 · Cited by 4,949
Kraken: ultrafast metagenomic sequence classification using exact alignments
Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology · doi:10.1186/gb-2014-15-3-r46 · Cited by 4,521
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180
Resolving difficult phylogenetic questions: Why more sequences are not enough
Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000602 · Cited by 1,129
Cited by
Whole Genome Phylogeny of Bacillus by Feature Frequency Profiles (FFP)
Wang, A., & Ash, G. J. (2015) · Scientific Reports · doi:10.1038/srep13644 · Cited by 517
Wang, Y., Zhang, R., Li, J., Wu, Z., Yin, W., Schwarz, S., Tyrrell, J. M., Zheng, Y., Wang, S., Shen, Z., et al. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.260 · Cited by 434
Cross-reactivity between tumor MHC class I–restricted antigens and an enterococcal bacteriophage
Fluckiger, A., Daillère, R., Sassi, M., Sixt, B. S., Liu, P., Loos, F., Richard, C., Rabu, C., Alou, M. T., Goubet, A.-G., et al. (2020) · Science · doi:10.1126/science.aax0701 · Cited by 396
Clermont, O., Dixit, O. V. A., Vangchhia, B., Condamine, B., Dion, S., Bridier‐Nahmias, A., Denamur, E., & Gordon, D. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14713 · Cited by 257
Inferring synteny between genome assemblies: a systematic evaluation
Liu, D., Hunt, M., & Tsai, I. J. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2026-4 · Cited by 147
Metadata
- Authors
- Treangen, T. J., Ondov, B., Koren, S., & Phillippy, A. M.
- Venue
- Genome biology
- Publisher
- BioMed Central
- Published
- 2014-01-01
- Volume
- 15
- Issue
- 11
- Pages
- 524-524
- ISSN
- 1465-6906 (ISSN-L)
- OpenAlex
- W2118442768
- Cited by
- 1,654
- References
- 18
- FWCI
- 22.39
- 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: The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. https://app.cochat.ai/papers/10.1186/preaccept-2573980311437212
- The paper
- Treangen, T. J., Ondov, B., Koren, S., & Phillippy, A. M. (2014). The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome biology. https://doi.org/10.1186/preaccept-2573980311437212
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.
