Biodi e si y In o ma ion Science and S anda ds 9: e175153
doi: 10.3897/biss.9.175153
Con e ence Abs ac
The Swedish Re e ence Genome Po al: A Hub o
Non-Human Euka yo ic Genomic Da a
Visualisa ion, Disco e y, and Reuse
Hen ik Lan z , Daniel B ink , Ro y C ean , Quen in Åg en , Hanna Kul ima , Beng Pe sson , Johan
Rung , Angela P. Fuen es-Pa do
‡ Na ional Bioin o ma ics In as uc u e Sweden, Science o Li e Labo a o y, Uppsala Uni e si y, Uppsala, Sweden
§ Science o Li e Labo a o y Da a Cen e, Uppsala Uni e si y, Uppsala, Sweden
| Science o Li e Labo a o y Da a Cen e, Swedish Museum o Na u al His o y, S ockholm, Sweden
Co esponding au ho : Hen ik Lan z (hen ik.lan z@scili elab.se),
Angela P. Fuen es-Pa do (ap [email protected])
Recei ed: 16 Oc 2025 | Published: 24 No 2025
Ci a ion: Lan z H, B ink D, C ean R, Åg en Q, Kul ima H, Pe sson B, Rung J, Fuen es-Pa do AP (2025) The
Swedish Re e ence Genome Po al: A Hub o Non-Human Euka yo ic Genomic Da a Visualisa ion, Disco e y,
and Reuse. Biodi e si y In o ma ion Science and S anda ds 9: e175153. h ps://doi.o g/10.3897/biss.9.175153
Abs ac
Non-human euka yo ic genome assemblies and anno a ions a e equen ly dispe sed
ac oss eposi o ies, supplemen a y ma e ials, o emain unpublished. Thei access o en
equi es echnical expe ise and la ge downloads, hinde ing usabili y. The Swedish
Re e ence Genome Po al* (SRGP) o e s a web pla o m o easily ind, explo e, and
sha e genomic da a om non-human euka yo ic species s udied in Sweden.
The SRGP ga he s assemblies and anno a ions in o species-speci ic pages wi h an
in e ac i e JB owse2 genome b owse , me ada a, and download links (Fig. 1). This web
in e ace p o ides use - iendly isualisa ions aimed a b oad use communi ies,
pa icula ly in biodi e si y and e olu ion.
Unlike global esou ces such as Ensembl o he UCSC Genome B owse , which ocus on
model o ganisms, he SRGP showcases species s udied in Swedish ins i u ions. I os e s
communi y-d i en da a sha ing and b oadens access o genomic anno a ions ha a e
a ely published (e.g., om popula ion genomics), while adhe ing o Findable,
‡ § § | § ‡
§ §
1
© Lan z H e al. This is an open access a icle dis ibu ed unde he e ms o he C ea i e Commons A ibu ion License (CC BY
4.0), which pe mi s un es ic ed use, dis ibu ion, and ep oduc ion in any medium, p o ided he o iginal au ho and sou ce a e
c edi ed.
Accessible, In e ope able and Reusable (FAIR) p inciples. In doing so, i b idges global
in as uc u es wi h local esea ch needs, enabling bo h specialis s and non-specialis s o
make be e use o genomic da a.
Figu e 1.
Home page and species pages o he Swedish Re e ence Genome Po al.
2Lan z H e al
The echnical a chi ec u e o he SRGP (Fig. 2) is designed o make he se ice easy o
use and euse by o he s:
•Simple and secu e: Buil wi h Hugo, a s a ic si e gene a o ha equi es no
da abases o hea y se e s, enabling ligh weigh main enance.
•Ligh weigh and as : Composed o p ebuil pages and iles o quick loading and
easy scalabili y.
•Open and eusable: Fully open-sou ce, allowing o he s o adap and ex end he
code.
•Easy o upda e: New species o da ase s can be added by edi ing con igu a ion
iles and ebuilding he si e.
•Po able: Packaged wi h Docke o easy deploymen anywhe e, including Kube
ne es clus e s.
•Use - iendly: In eg a es JB owse2 o in e ac i e explo a ion o genomic da a.
Figu e 2.
Swedish Re e ence Genome Po al a chi ec u e and da a low, by SciLi eLab Da a Cen e
(2025), license CC BY 4.0.
1. Use s submi species in o ma ion, da a acks, and an image o SciLi eLab.
2. Da a a e e ched om public eposi o ies.
3. Species pages a e c ea ed, and da a a e in eg a ed in o he genome b owse .
4. Webpages a e openly accessible online.
The Swedish Re e ence Genome Po al: A Hub o Non-Human Euka yo ic Genomic ... 3
The SRGP is designed o simple deploymen and main enance. Genome da a and
anno a ions a e p ocessed wi h au oma ed sc ip s in Docke con aine s o ensu e
consis ency and ep oducibili y. The websi e is buil wi h Hugo, which gene a es as ,
ligh weigh pages equi ing no da abase. Bo h da a and pages a e bundled in o Docke
images and deployed on a Kube ne es clus e , wi h A goCD handling upda es
au oma ically. This se up p o ides eliable ope a ion on s anda d in as uc u e, easy
scaling o new da ase s, and secu e, low-main enance access o genomic esou ces
(Fig. 2).
In summa y, he SRGP makes p e iously hidden genomic da a, especially om local o
specialised communi ies, easy o ind and explo e h ough a single, use - iendly
b owse . I lowe s access ba ie s while emaining simple, as , and scalable. By uni ying
sca e ed esou ces, i p o ides a eusable model o o he coun ies, ins i u ions, o
esea ch g oups. This p esen a ion is a ailable in (p esen ación disponible en español
en) Fuen es‐Pa do e al. (2025).
Keywo ds
assembly, genome b owse , genomic anno a ion, JB owse2, open sou ce, open science,
da a isualisa ion
P esen ing au ho
Angela P. Fuen es‐Pa do
P esen ed a
Li ing Da a 2025
Acknowledgemen s
This wo k is de eloped and ope a ed by Science o Li e Labo a o y (SciLi eLab) Da a
Cen e, wi h suppo om he SciLi eLab & Wallenbe g Na ional P og am o Da a-D i en
Li e Science and he Swedish Founda ion o S a egic Resea ch (SSF). The SciLi eLab
Da a Cen e ex ends i s g a i ude o na ional and in e na ional eposi o ies, including he
Eu opean Nucleo ide A chi e (ENA), Na ional Cen e o Bio echnology In o ma ion
(NCBI), SciLi eLab Da a Reposi o y, Swedish Biodi e si y Da a In as uc u e, SLU
Swedish Species In o ma ion Cen e, Genomes on a T ee (GoaT), Global Biodi e si y
In o ma ion Facili y (GBIF), and IUCN Red Lis o Th ea ened Species, om which i
e ie es da a. These esou ces enable esea che s and he wide communi y o access
aluable in o ma ion openly. We a e also g a e ul o he open-sou ce so wa e ha was
c ucial o he de elopmen o his web pla o m, including Hugo, Boo s ap, Lea le ,
JB owse2, SAM ools, GNU Make, and Kube ne es.
4Lan z H e al
*1
Con lic s o in e es
The au ho s ha e decla ed ha no compe ing in e es s exis .
Re e ences
• Fuen es‐Pa do A, B ink D, C ean R, Åg en Q, Kul ima H, Pe sson B, Rung J, Lan z H
(2025) P esen a ion o he Swedish Re e ence Genome Po al a he Li ing Da a 2025
con e ence - P esen ación del Po al Sueco de Genomas de Re e encia en la con e encia
Da os Vi os 2025. Uppsala Uni e si y. P esen a ion. h ps://doi.o g/10.17044/scili elab.
30218329
Endno es
h ps://genomes.scili elab.se/
The Swedish Re e ence Genome Po al: A Hub o Non-Human Euka yo ic Genomic ... 5
