Citing nf-LO

To cite nf-LO, please refer to:

nf-LO: A scalable, containerised workflow for genome-to-genome lift over
Andrea Talenti, James Prendergast
Genome Biology and Evolution, 2021;, evab183, https://doi.org/10.1093/gbe/evab183

References

nf-LO relies on a series of dependencies, includin:

  1. Adaptive seeds tame genomic sequence comparison. Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Genome Res. 2011 21(3):487-93; http://dx.doi.org/10.1101/gr.113985.110

  2. Harris, R.S. (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University

  3. Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100. http://dx.doi.org/10.1093/bioinformatics/bty191

  4. Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64

  5. Zhao, H., Sun, Z., Wang, J., Huang, H., Kocher, J.-P., & Wang, L. (2013). CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics (Oxford, England), btt730

  6. Lin, HN., Hsu, WL. GSAlign: an efficient sequence alignment tool for intra-species genomes. BMC Genomics 21, 182 (2020). https://doi.org/10.1186/s12864-020-6569-1