References

Review on genome assembly with Long Reads

• 2024 review - https://www.nature.com/articles/s41576-024-00718-w
• Vertebrate Genomes Project CLR assemblies - https://www.nature.com/articles/s41586-021-03451-0

Historical

First human genome

• Nature - 2001 https://www.nature.com/articles/35057062
• Science - 2001 https://www.nature.com/scitable/content/Initial-sequencing-and-analysis-of-the-human-16729/
• The (near) complete sequence of a human genome https://genomeinformatics.github.io
• The complete sequence of a human genome https://www.science.org/doi/10.1126/science.abj6987
• Semi-automated assembly of high-quality diploid human reference genomes https://www.nature.com/articles/s41586-022-05325-5
• Telomere-to-telomere assembly of a complete human X chromosome https://www.nature.com/articles/s41586-020-2547-7
• The complete sequence of a human Y chromosome https://www.nature.com/articles/s41586-023-06457-y
• Telomere-to-telomere assembly of diploid chromosomes with Verkko https://www.nature.com/articles/s41587-023-01662-6

Repeats

• https://science.sciencemag.org/content/338/6108/758

Assembly Graphs

• https://link.springer.com/article/10.1007/s40484-019-0181-x
• https://academic.oup.com/bfg/article/11/1/25/191455

Kmer analysis

• Review on kmer analysis https://arxiv.org/abs/2404.01519
• Build a Meryl database https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs
• Merqury https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02134-
• KAT https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408915/pdf/btw663.pdf
• Genomescope https://www.nature.com/articles/s41467-020-14998-3
• Bernardo Cavijo’s post https://bioinfologics.github.io/post/2018/09/17/k-mer-counting-part-i-introduction/

Assemblers

• HiFiAdapterFilt https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08375-1
• Hicanu https://genome.cshlp.org/content/early/2020/08/14/gr.263566.120
• Hifiasm [https://arxiv.org/pdf/2008.01237.pdf](https://www.nature.com/articles/s41592-020-01056-5
• Trio Binning https://www.nature.com/articles/nbt.4277
• Falcon and Falcon-Unzip https://www.nature.com/articles/nmeth.4035
• HiFi Reads https://www.nature.com/articles/s41587-019-0217-9

Purging assemblies

• Purge Haplotigs https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2485-7
• Purge Dups https://academic.oup.com/bioinformatics/article/36/9/2896/5714742
• Widespread false gene gains caused by duplication errors in genome assemblies https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02764-1

Hi-C

• Hi-C is invented https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2858594/pdf/nihms-194459.pdf
• SALSA2 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007273
• YaHS https://www.biorxiv.org/content/10.1101/2022.06.09.495093v1
• Hi-C https://pubmed.ncbi.nlm.nih.gov/22652625/
• More on chromatin structure https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040307/
• 3C versus DNA FISH https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1081-2
• FISH and Hi-C https://www.nature.com/articles/s41467-019-10005-6

Curation with Hi-C

• Grit Team video on Pretext and Hi-C Video
• Hi-C for Dummies Slides

Pipelines for genome assembly

• Pipeasm - https://www.biorxiv.org/content/10.1101/2024.10.21.598381v1
• Colora - https://www.biorxiv.org/content/10.1101/2024.09.10.612003v1
• Galaxy VGP Pipeline - https://www.nature.com/articles/s41587-023-02100-3