https://doi.org/10.5281/zenodo.8175416
Detailed description:
A.oxysepala_contig_draft.fa: The original draft contigs of A.oxysepala for CRAQ-correct performing.
A.oxysepala_contig_CRAQcorrect.fa: The new generated A.oxysepala contigs after splitting misjoins at CSE positions.
A.oxysepala_original.scaffold.hic.fas: The original scaffolds from the draft contigs of A.oxysepala. 3D-DNA pipeline (without correction: -r 0) was performed for the De novo scaffolding process.
A.oxysepala_corrected.scaffold.hic.fas: The new generated scaffolds from the CRAQ-corrected contigs of A.oxysepala. 3D-DNA pipeline (without correction: -r 0) was performed for the De novo scaffolding process as above.
HiC-contacts-for-original-scaffold: A folder that contains the results, including the Hi-C interaction file (.hic), and the orientation and order information (.assembly) file for checking up the anchored draft contigs. These files can be loaded directly into the Juicebox tool for visualization
HiC-contacts-for-corrected-scaffold: A folder that contains results, including the Hi-C interaction file (.hic), and the orientation and order information (.assembly) file for checking up the anchored CRAQ-corrected contigs. These files can be loaded directly into the Juicebox tool for visualization.
A.oxysepala_DLE-1_optical.cmap: De novo assembled Bionano optical DLE-1 consensus maps (.cmap) of A.oxysepala for detecting and validating potentail problematic contigs in this project. We in silico digested the initial draft contigs and CRAQ-corrected contigs of A.oxysepala using the same restriction enzyme DLE-1 ('CTTAAG') to produce genomic maps.
Bionano_cmap_VS_draft_Aox.alignref: A folder that contains the alingment results by aligning the in silico DLE-1 genomic maps of the initial A.oxysepala contigs to the Bionano optical consensus maps. These results can be loaded directly into Bionano Access tool for visualization.
Bionano_cmap_VS_corrected_Aox.alignref: A folder that contains the alingment results by aligning the in silico genomic maps of the CRAQ-corrected A.oxysepala contigs to the Bionano optical consensus maps. These results can be loaded directly into Bionano Access tool for visualization.
Raw_sequencing_Illumina_PacBio_HiC.link: An address that links all of the raw sequencing data used in this project, including the raw PacBio CLR long-reads, the Illumina PE-reads, and Hi-C data. These sequencing data have also been submitted to the National Center for Biotechnology Information (NCBI) under the BioProject Accession: PRJNA636213.