Domestic guinea pig (Cavia porcellus)
Guinea pigs sleep with their eyes open! Read more about domestic guinea pigs in Wikipedia.
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Chromosome-length genome assembly
Download the Cavpor3.0_HiC.fasta.gz file containing the chromosome-length (2n=64) assembly of the domestic guinea pig genome. All modifications with respect to the draft (see below) are annotated in the Cavpor3.0_HiC.assembly file. Some basic stats associated with the new reference, Cavpor3.0_HiC, are listed below. The full data release can be explored here.
Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
The chromosome-length genome assembly is based on the draft assembly Cavpor3.0 (GCF_000151735.1), credited below.
3D Assembly was performed using 3D-DNA pipeline (Dudchenko et al., Science, 2017). The genome was reviewed using Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018). See Methods for more information.
The blood sample for in situ Hi-C preparation was donated by a female individual, and provided to us by Rockland Immunochemicals Inc. We thank BioChemed Services for additional samples for this species.
Hi-C Contact maps
Hi-C data was aligned to the draft reference using Juicer (Durand, Shamim et al., Cell Systems, 2016), and contact maps visualizing the alignments with respect to the draft and the new reference were built using 3D-DNA (Dudchenko et al., Science, 2017). The contact maps can be explored below via Juicebox.js interactive tool (Robinson et al., Cell Systems, 2018). (Please note that the interactive figures are scaled 1:2.) To explore the assembly in greater detail, please download the .hic and .assembly files from the data release folder and use Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018).
If you use this genome assembly in your research, please check that the conditions of use associated with the draft permit it, and acknowledge the following work.
Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95. https://doi.org/10.1126/science.aal3327.
Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.
This is a work in progress. If you notice any discrepancies in the map or have data that confirms or contradicts the suggested reference, please email us at firstname.lastname@example.org or leave a comment on the Forum.