The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
GFF Utilities: GffRead and GffCompare
Open accessAbstract
Summary: GTF (Gene Transfer Format) and GFF (General Feature Format) are popular file formats used by bioinformatics programs to represent and exchange information about various genomic features, such as gene and transcript locations and structure. GffRead and GffCompare are open source programs that provide extensive and efficient solutions to manipulate files in a GTF or GFF format. While GffRead can convert, sort, filter, transform, or cluster genomic features, GffCompare can be used to compare and merge different gene annotations. Availability and implementation: GFF utilities are implemented in C++ for Linux and OS X and released as open source under an MIT license ( https://github.com/gpertea/gffread , https://github.com/gpertea/gffcompare ).
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.
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?
To assess the accuracy of the mapping, gffcompare was used to compare our annotations to the reference annotation.
“To assess the accuracy of the mapping we used gffcompare (v0.11.2) (Pertea & Pertea 2020) to compare our annotations to the reference annotation.”
From Parallel molecular mechanisms underlie convergent evolution of the exaggerated snout phenotype in East African cichlids (2022) · cites this paper as Pertea & Pertea 2020
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
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Self-citationPertea, M., Shumate, A., Pertea, G., Varabyou, A., Breitwieser, F. P., Chang, Y.-C., Madugundu, A. K., Pandey, A., & Salzberg, S. L. (2018) · Genome Biology · doi:10.1186/s13059-018-1590-2 · Cited by 335
Self-citation
Flagged first, then by citations
Research works printed but not linked: 25
- J Yoshimura, 2019, Recompleting the Caenorhabditis elegans genome., Genome Res., 29, 1009-1022, 10.1101/gr.244830.118 · DOI
- A Zimin, 2014, A new rhesus macaque assembly and annotation for next-generation sequencing analyses., Biol Direct., 9, 10.1186/1745-6150-9-20 · DOI
- C Boschiero, 2019, Identification and Functional Investigation of Genome-Encoded, Small, Secreted Peptides in Plants., Curr Protoc Plant Biol., 4, e20098, 10.1002/cppb.20098 · DOI
- T Chang, 2018, High-Throughput Characterization of Primary microRNA Transcripts., Methods Mol Biol., 1823, 1-9, 10.1007/978-1-4939-8624-8_1 · DOI
- L Han, 2019, RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize., Methods Mol Biol., 1933, 67-86, 10.1007/978-1-4939-9045-0_4 · DOI
- P Jain, 2017, Identification of long non-coding RNA in rice lines resistant to Rice blast pathogen Maganaporthe oryzae., Bioinformation., 13, 249-255, 10.6026/97320630013249 · DOI
- X Liu, 2019, Long non-coding and coding RNA profiling using strand-specific RNA-seq in human hypertrophic cardiomyopathy., Sci Data., 6, 90, 10.1038/s41597-019-0094-6 · DOI
- Y Lv, 2016, Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.)., BMC Genomics., 17, 10.1186/s12864-016-2650-1 · DOI
- G Sablok, 2019, NAMS: Noncoding Assessment of long RNAs in Magnoliophyta Species., Methods Mol Biol., 1933, 257-264, 10.1007/978-1-4939-9045-0_15 · DOI
- F Song, 2019, Long noncoding RNA and mRNA expression profiles following igf3 knockdown in common carp, Cyprinus carpio., Sci Data., 6, 10.1038/sdata.2019.24 · DOI
- S Sreenivasamurthy, 2017, Mosquito-Borne Diseases and Omics: Tissue-Restricted Expression and Alternative Splicing Revealed by Transcriptome Profiling of Anopheles stephensi., OMICS., 21, 488-497, 10.1089/omi.2017.0073 · DOI
- A Stroehlein, 2018, The small RNA complement of adult Schistosoma haematobium., PLoS Negl Trop Dis., 12, e0006535, 10.1371/journal.pntd.0006535 · DOI
- H Sun, 2019, Bioinformatics Approaches to Studying Plant Long Noncoding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-Seq Data Sets., Methods Mol Biol., 1933, 197-205, 10.1007/978-1-4939-9045-0_11 · DOI
- S Kovaka, 2019, Transcriptome assembly from long-read RNA-seq alignments with StringTie2., Genome Biol., 20, 278, 10.1186/s13059-019-1910-1 · DOI
- N Manchanda, 2020, GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations., BMC Genomics., 21, 193, 10.1186/s12864-020-6568-2 · DOI
- M Shao, 2017, Accurate assembly of transcripts through phase-preserving graph decomposition., Nat Biotechnol., 35, 1167-1169, 10.1038/nbt.4020 · DOI
- A Azlan, 2019, Systematic identification and characterization of Aedes aegypti long noncoding RNAs (lncRNAs)., Sci Rep., 9, 12147, 10.1038/s41598-019-47506-9 · DOI
- E Chow, 2019, Characterization of Hepatocellular Carcinoma Cell Lines Using a Fractionation-Then-Sequencing Approach Reveals Nuclear-Enriched HCC-Associated lncRNAs., Front Genet., 10, 1081, 10.3389/fgene.2019.01081 · DOI
- Y Niknafs, 2017, TACO produces robust multisample transcriptome assemblies from RNA-seq., Nat Methods., 14, 68-70, 10.1038/nmeth.4078 · DOI
- J Vadnal, 2018, Refined ab initio gene predictions of Heterorhabditis bacteriophora using RNA-seq., Int J Parasitol., 48, 585-590, 10.1016/j.ijpara.2018.02.001 · DOI
- M Burset, 1996, Evaluation of gene structure prediction programs., Genomics., 34, 353-67, 10.1006/geno.1996.0298 · DOI
- T Cormen, 2009, Introduction to Algorithms, 3rd Edition.
- G Pertea, 2020, gpertea/gclib: v0.11.9 (Version v0.11.9)., Zenodo.
- G Pertea, 2020, gpertea/gffread: v0.11.8 (Version v0.11.8)., Zenodo.
- G Pertea, 2020, gpertea/gffcompare: v0.11.6 (Version v0.11.6)., Zenodo.
Cited by
Sorted by citations
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129
Segmental duplications and their variation in a complete human genome
Vollger, M. R., Guitart, X., Dishuck, P. C., Mercuri, L., Harvey, W. T., Gershman, A., Diekhans, M., Sulovari, A., Munson, K. M., Lewis, A. P., et al. (2022) · Science · doi:10.1126/science.abj6965 · Cited by 350
Vascular Disease and Thrombosis in SARS-CoV-2-Infected Rhesus Macaques
Aid, M., Busman-Sahay, K., Vidal, S. J., Maliga, Z., Bondoc, S., Starke, C., Terry, M., Jacobson, C. A., Wrijil, L., Ducat, S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.005 · Cited by 215
Xia, X., Zhang, F., Li, S., Luo, X., Peng, L., Dong, Z., Pausch, H., Leonard, A. S., Crysnanto, D., Wang, S., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03052-2 · Cited by 53
Highly accurate isoform identification for the human transcriptome
Sommer, M. J., Cha, S., Varabyou, A., Rincon, N., Park, S., Minkin, I., Pertea, M., Steinegger, M., & Salzberg, S. L. (2022) · doi:10.1101/2022.06.08.495354 · Cited by 40
Self-citationAlexander, H., Hu, S. K., Krinos, A. I., Pachiadaki, M., Tully, B. J., Neely, C. J., & Reiter, T. (2021) · doi:10.1101/2021.07.25.453713 · Cited by 67
Chakraborty, S., Wenzlitschke, N., Anderson, M. J., Eraso, A., Baudic, M., Thompson, J. J., Evans, A. A., Shatford-Adams, L. M., Chari, R., Awasthi, P., et al. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.02.002 · Cited by 22
Annotation matters: the effect of structural gene annotation on orthology inference
Prieto-Baños, S., Nevers, Y., Altenhoff, A., Warwick Vesztrocy, A., Dessimoz, C., & Glover, N. M. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf365 · Cited by 19
Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle
Xia, X., Wang, F., Luo, X., Li, S., Lyu, Y., Zheng, Y., Ma, Z., Qu, K., Song, R., Liu, J., et al. (2025) · Advanced Science · doi:10.1002/advs.202503258 · Cited by 14
Song, G.-Y., Guo, X.-N., Yao, J., Lu, Z.-N., Xie, J.-H., wu, F., He, J., Fu, Z.-L., & Han, J. (2023) · BMC Cardiovascular Disorders · doi:10.1186/s12872-023-03311-x · Cited by 11
Helmy, M., Li, J. U., Yan, X. F., Meade, R. K., Anderson, E., Chen, P. B., Czechanski, A. M., Di Domenico, T., Flint, J., Garrison, E., et al. (2026) · Cell Genomics · doi:10.1016/j.xgen.2025.101074 · Cited by 2
Duenser, A., Singh, P., Lecaudey, L. A., Sturmbauer, C., Albertson, C., Gessl, W., & Ahi, E. P. (2022) · bioRxiv · doi:10.1101/2022.01.13.476207 · Cited by 1
“11.2) (Pertea & Pertea 2020) to compare our annotations to the reference annotation.”
BackgroundInfluential
Metadata
- Authors
- Pertea, G., & Pertea, M.
- Affiliations
- Johns Hopkins University (US)
- Corresponding author
- Pertea, Mihaela
- Venue
- F1000Research
- Publisher
- F1000 Research Ltd
- Published
- 2020-09-09
- Volume
- 9
- Pages
- 304
- ISSN
- 2046-1402 (ISSN-L)
- PMC
- PMC7222033
- OpenAlex
- W3022572641
- Cited by
- 1,152
- References
- 3
- Citations by year
- 2026: 169 · 2025: 208 · 2024: 264 · 2023: 206 · 2022: 155 · 2021: 125 · 2020: 25
- FWCI
- 41.85
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- F1000Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. National Institutes of Health (R01-HG006677)
- National Science Foundation (DBI-1759518)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- GFF, GTF, genome annotation, annotation comparison, open-source bioinformatics software
- MeSH terms
- Software, Genome, Computational Biology, Genomics, Molecular Sequence Annotation
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
