Relevant papers

[hyanwong]

Just an issue to collect any relevant papers. For example, there's a whole Genome Biology issue on graph genomes at

https://www.biomedcentral.com/collections/graphgenomes (also see "Pangenome Graphs" Annu. Rev. Genomics Hum. Genet. 21, 139–162 (2020).)

Here's one about nested trees which might be interesting.

"Unsorted Homology within Locus and Species Trees": https://academic.oup.com/sysbio/article/63/6/988/2847747?login=false

The most recent high impact publication is the Nature one from May 2023:

"A draft human pangenome reference": https://www.nature.com/articles/s41586-023-05896-x#Sec7

[hyanwong]

Re simulating SVs, in a thread on slack, Ben Haller, Kevin, and Nate pointed out these:

Foward-simulation:

• Inversions: Schaal, Haller, Lotterhos (2022): doi: 10.1098/rstb.2021.0200

Backward simulation:

• CNVs: Thornton K R (2007) The neutral coalescent process for recent gene duplications and copy-number variants. Genetics 177: 987–1000; Teshima & Innan (2012) The Coalescent with Selection on Copy Number Variants; Otto & Wiehe(2023) The structured coalescent in the context of gene copy number variation
• Inversions: Guerrera, Rousset, Kirkpatrick (2012) Coalescent patterns for chromosomal inversions in divergent populations doi: 10.1098/rstb.2011.0246

  Inference (e.g. SV spotting):

  Yan at al (2021): https://elifesciences.org/articles/67615

Genome graphs

• "Genome graphs and the evolution of genome inference" Paten et al, Genome research 2017
• The Computational Pan-Genomics Consortium 2018 Computational pan-genomics: status, promises and challenges (especially the "Data structures" section)

[duncanMR]

Here are some additional references I found:

Forward simulation

Ben Haller mentioned that the Lotterhos group has two papers on inversions with SLiM. I think this is the second one:

• "The Effect of Neutral Recombination Variation on Genome Scans for Selection", Lotterhos, K.E. (2019), https://academic.oup.com/g3journal/article/9/6/1851/6028019

Backward simulation

Here is another backward time simulator with inversions:

• "A sequential coalescent algorithm for chromosomal inversions", Peischl et al. (2013), doi:10.1038/hdy.2013.38

Structural variation

This is a thorough and up-to-date review of SVs in general:

• "Structural variation in the sequencing era", Ho, Uran and Mills (2020), https://doi.org/10.1038/s41576-019-0180-9

[hyanwong]

Here's an interesting simulator that seems to do all sorts of SV stuff: It's a bit old now though.

"ALF—A Simulation Framework for Genome Evolution": Dalquen et al (2012) https://academic.oup.com/mbe/article/29/4/1115/1188345

I found it via https://www.biorxiv.org/content/10.1101/2024.08.28.610045v1

[duncanMR]

Here's an interesting simulator that seems to do all sorts of SV stuff: It's a bit old now though.

"ALF—A Simulation Framework for Genome Evolution": Dalquen et al (2012) https://academic.oup.com/mbe/article/29/4/1115/1188345

I found it via https://www.biorxiv.org/content/10.1101/2024.08.28.610045v1

Oh yeah, I found this in my initial review; it's impressive how many processes they simulate, although the reliance on a species tree is a pity.