Genome assembly

Sequencing technology evolution toward long high quality reads enables today to assemble large genomes (1Gb and more) for a few thousand euros. Which makes it possible for a team or even a single researcher to produce the reference best adapted for her/his daily work. Genome assembly is know to be like building a jigsaw puzzle, the larger the pieces the easier the work. Long read assembly will produce contigs which depending on the read quality will have to be corrected (Nanopore or PacBio CLR) or not (PacBio HiFi). Contig correction is performed by aligning long and/or short reads and updating bases in the reference which do not match with the alignment. Contigs are then scaffolded in chromosomes using BioNano optical maps, Hi-C ligation reads or a genetic map.
Sigenae has assembled over fifteen fish genome as well as the bee genome. Some of these assemblies where quite complicated due to slow evolution and recent duplication as for example the sterlet sturgeon genome (Nature Ecology & Evolution, 2020). We have taken part in the assemblies of the SeqOccin project. And we have also been in charge of the assemblies of the GenoFish project of which some genomes are references at the NCBI or Ensembl like the javafish, the yellow perch or the european perch.

Assembly projects recently published