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Fig. 4 | GigaScience

Fig. 4

From: LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

Fig. 4

LINKS re-scaffolding of the white spruce (P. glauca, PG29 cultivar) genome with k-mer pairs derived from the white spruce WS77111 genotype draft assembly. Iterative LINKS scaffolding rounds (v1.1 with fourteen iterations, k = 26, t = 200 to 50, l = 5, a = 0.3, d = 5 kbp to 100kbp, interval shown on x axis, solid black line) were performed on the PG29 V3 ABySS assembly sequence scaffolds (Genbank: GCA_000411955.3, 4.2 M scaffolds ≥ 500 bp, bottom left panel, red line) using sequence data from the WS77111 V1 draft assembly (Genbank: PRJNA242552, 4.3 M scaffolds ≥ 500 bp, top left panel, blue line), making 84,529 total merges (top right panel) and increasing the PG29 assembly contiguity 1.5-fold to reach an NG50 length [23] of 114,888 bp (4.1 M scaffolds ≥ 500 bp; top left panel). We have validated the final LINKS assembly of spruce with scalable gap-filling software Sealer [34] and MPET reads from 4, 8 and 12kbp libraries (bottom left panel). Validation with the latter and its diminished return with large k-mer intervals tracks with the increase in gap lengths (bottom right panel). We note that LINKS re-scaffolding of the white spruce assembly was done to demonstrate scalability

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