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Fig. 1 | BMC Biology

Fig. 1

From: Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution

Fig. 1

Outline of the assembly process. Hi-C data were used to scaffold the original ALLPATHS-LG assembly (SRA1) to produce the first proximity-guided assembly (PGA1). Gaps within PGA1 were filled using PacBio long reads with PBJelly and polished with Quiver and Pilon to produce PGA1.5. This gap-filled assembly was then broken at sequence gaps, rescaffolded with the Hi-C data, gap-filled with PBJelly, and polished with Quiver and Pilon to produce the final assembly (PGA2). To illustrate the utility of the Hi-C data, SRA1 was also combined with the PacBio data alone (without Hi-C data) to produce the hybrid assembly APS1. Summary statistics are provided in boxes next to each assembly, and the improvements of PGA1 and PGA2 relative to the input assemblies are provided in red and blue boxes, respectively. sN50 and sL50 denote the scaffold N50 size and length, respectively. HQ indicates the number or length of scaffolds that were determined to have high quality clustering and orientation within the assembly

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