References
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
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
- 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