Linked-read sequencing enables haplotype-resolved resequencing at population scale
Cite this dataset
Lutgen, Dave et al. (2020). Linked-read sequencing enables haplotype-resolved resequencing at population scale [Dataset]. Dryad. https://doi.org/10.5061/dryad.9zw3r22bf
Abstract
Methods
10X Genomics linked-reads (60x coverage) were assembled using the Supernova 2.1 assembler. To remove duplicate scaffolds of at least 99% identity from the pseudohaploid assembly, we ran the dedupe procedure in BBTools (https://sourceforge.net/projects/bbmap/) allowing up to 7,000 edits. This reduced the assembly to 11,030 scaffolds. We then aimed to ensure that all duplicate scaffolds were removed and retain only scaffolds whose integrity can be confirmed by the presence of syntenic regions in another songbird genome. To this end, we performed a lastz alignment against the collared flycatcher assembly version 1.5, which is the highest-quality assembly available from the Muscicapidae family. For this we used lastz 1.04 with settings M=254, K=4500, L=3000, Y=15000, C=2, T=2, and --matchcount=10000. This resulted in 295 scaffolds with unique hits in the flycatcher assembly.
Funding
German Research Foundation, Award: BU3456/3-1
Science for Life Laboratory Swedish Biodiversity Program, Award: 2015-R14
Deutsche Forschungsgemeinschaft, Award: BU3456/3-1
Science for Life Laboratory Swedish Biodiversity Program, Award: 2015-R14