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Red raspberry (Rubus idaeus)

The species name, idaeus, is a reference to Mount Ida in Greece where raspberries are believed to be discovered. Read more about red raspberries on the Missouri Botanical Garden's website.


'Anitra' Red raspberry, Graminor Ltd.

Chromosome-length genome assembly

Download the AnitraCuratedED_HiC.fasta.gz file containing the chromosome-length (2n=14) assembly of the red raspberry genome. All modifications with respect to the draft (see below) are annotated in the AnitraCuratedED_HiC.assembly file. Some basic stats associated with the new reference, AnitraCuratedED_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 AnitraCuratedED, credited below.

This draft assembly was made in a collaborative effort by Jahn Davik (NIBIO), Daniel James Sargent (NIAB-EMR), Dag Røen (Graminor Ltd.), and Muath Alsheikh (Graminor Ltd.)


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.

Hi-C sample

The sample for in situ Hi-C preparation was obtained from Graminor Ltd. (Norway).

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). 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.

This draft assembly was made in a collaborative effort by Jahn Davik (NIBIO), Daniel James Sargent (NIAB-EMR), Dag Røen (Graminor Ltd.), and Muath Alsheikh (Graminor Ltd.)

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.

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.


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 or leave a comment on the Forum.

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