Availability
Ocean Read Atlas is freely-available at: https://ocean-read-atlas.mio.osupytheas.fr/.
Publication
Lemane, T., Lezzoche, N., Lecubin, J., Pelletier, E., Lescot, M., Chikhi, R., & Peterlongo, P. (2023). kmindex and ORA: indexing and real-time user-friendly queries in terabytes-sized complex genomic datasets. bioRxiv, 2023-05.
Selected excerpts
“[…] we introduce the publicly accessible web server “Ocean Read Atlas” (ORA) at https://ocean-read-atlas.mio.osupytheas.fr/, which enables real-time queries on the entire Tara Oceans dataset. […]”
” […] we built and made available a public web interface able to perform queries on a dataset composed of 1,393 samples (distinct locations and distinct fraction sizes) of the Tara Oceans project. These samples are divided into six distinct groups, determined by the size fraction of the sequenced species. Based on this clustering we built six distinct indexes (all with the same parameters). At query time, as all the six indexes are registered in a unique meta-index, the whole set of samples is queried.”
” The user can use one or more sequences to query the index and determine the similarity of each sequence to the 1,393 indexed samples. A world map depicts the resulting biogeography, as well as the environmental parameters associated with the sequences. Finally, results can be downloaded in the form of tables or under several image formats.”