Scaffolding Accuracy of Assemblies

Of our 103 A. thaliana assemblies, we highlighted the runtime and scaffolding accuracy of the assembly representing the TFÄ 04 accession (SRR1945711). This assembly was assembled with SPAdes (see below) and had a scaffold N50 of 120,255 bp with a total size of 115,803,138 bp [43 (link)]. Additionally, to demonstrate the scaffolding of a mammalian-sized genome, we used RaGOO to order and orient the mixed haplotype human Canu assembly derived from Pacific Biosciences CCS reads. This human assembly had a contig N50 of 22,778,121 bp and a total size of 3,418,171,375 bp. For both the TFÄ 04 and human assemblies, default RaGOO parameters were used and the software was run with 8 threads (“-t 8”). The TAIR 10 and hs37d5 reference genomes were used to scaffold the TFÄ 04 and human assemblies, respectively. RaGOO completed in 12.576 s and 12 min and 33.090 s for TFÄ 04 and human, respectively. The dotplots for both assemblies were made by aligning RaGOO pseudomolecules to the respective reference genomes with nucmer (-l 200 -c 500). Alignments were filtered with delta filter (-1 -l 20000), and plots were made with Mummerplot (--fat). Only nuclear chromosome and non-alternate sequences are shown in the dotplots.