Callithrix jacchus strain:cj1700 Genome sequencing and assembly

The female white-tufted marmoset (Callithrix jacchus) DNA was derived from a cell line (cj1700) of a single skin biopsy. Sequences were generated on the Pacific Biosciences Sequel instrument (V2 chemistry) to approximately 70x genome coverage based on a genome size estimate of 3 Gb. All SMRT sequences were assembled with FALCON-Integrate v1.7.5 then error corrected using the Arrow error-correction module. Additional polishing of the assembly for residual indels was done by alignment of 40x coverage of Illumina data followed by application of the Pilon algorithm. Finally, residual indels were detected and corrected using a custom pipeline in the lab of Dr. Evan Eichler. All detected chimeric contigs were broken using automated and manual processes using a same DNA source BioNano map as guidance. Chromosomal level scaffolds/contig files were generated by alignment to Bionano mapping data, the human genome and marmoset/human maps (Mariano Rocchi), and to the prior Callithrix jacchus 3.2 reference.