ntLink is a flexible de novo genome scaffolding toolkit which can be run in various modes depending on the desired user output, with multiple new functionalities recently introduced. Here, we provide the baseline assembly datasets used in the ntLink protocol paper "ntLink: a toolkit for de novo genome assembly scaffolding and mapping using long reads". The provided assemblies are ABySS (short-read) and Flye (long-read) assemblies of Caenorhabditis elegans genome sequencing data. The ABySS (v2.1.4) assembly utilized paired-end short reads (accession DRR008444), and was run with the following parameters: k=64 l=40 s=1000 q=15 B=10G j=8 kc=3 H=4 S=1000-10000 N=9.The C. elegans Flye (v2.5) assembly was run using Oxford Nanopore long reads (accession SRR10028109) and the following parameters: --nano-raw SRR10028109.fastq -g100m -t48.

{"references": ["Jackman, S. D., Vandervalk, B. P., Mohamadi, H., Chu, J., Yeo, S., Hammond, S. A., Jahesh, G., Khan, H., Coombe, L., Warren, R. L., & Birol, I. (2017). ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter. Genome Research, 27(5), 768\u2013777. https://doi.org/10.1101/gr.214346.116", "Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology, 37(5), 540\u2013546. https://doi.org/10.1038/s41587-019-0072-8"]}