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2012 FreeBayes

Garrison, E. and Marth, G., 2012. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907.

2013 FALCON, FALCON-unzip, FALCON-Phase

Chin, C.S., Alexander, D.H., Marks, P., Klammer, A.A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E.E. and Turner, S.W., 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature methods, 10(6), pp.563-569.
Chin, C.S., Peluso, P., Sedlazeck, F.J., Nattestad, M., Concepcion, G.T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A. and Cramer, G.R., 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nature methods, 13(12), pp.1050-1054.
Kronenberg, Z.N., Rhie, A., Koren, S., Concepcion, G.T., Peluso, P., Munson, K.M., Porubsky, D., Kuhn, K., Mueller, K.A., Low, W.Y. and Hiendleder, S., 2021. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nature communications, 12(1), pp.1-10.

2020 Merqury

Rhie, A., Walenz, B.P., Koren, S. and Phillippy, A.M., 2020. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome biology, 21(1), pp.1-27.

2021 merfin, mitoVGP

Formenti, G., Rhie, A., Walenz, B.P., Thibaud-Nissen, F., Shafin, K., Koren, S., Myers, E.W., Jarvis, E.D. and Phillippy, A.M., 2021. Merfin: improved variant filtering and polishing via k-mer validation. bioRxiv.
Formenti, G., Rhie, A., Balacco, J., Haase, B., Mountcastle, J., Fedrigo, O., Brown, S., Capodiferro, M.R., Al-Ajli, F.O., Ambrosini, R. and Houde, P., 2021. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome biology, 22(1), pp.1-22.
Rhie, A., McCarthy, S.A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J. and Lee, C., 2021. Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), pp.737-746.

2021 ag100pest update

Childers, A.K., Geib, S.M., Sim, S.B., Poelchau, M.F., Coates, B.S., Simmonds, T.J., Scully, E.D., Smith, T.P., Childers, C.P., Corpuz, R.L. and Hackett, K., 2021. The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. Insects, 12(7), p.626.
- Figure 1: general workflow
- Bioproject: https://www.ncbi.nlm.nih.gov/bioproject/555319
- "Ag100Pest began by using continuous long reads (CLRs) for assembly (details not presented herein) as the improved HiFi procedure [33] had not yet been developed"