20230912 Discussion enhancements meeting - notes to remember

[evezeyl]

Present meeting: Thomas, Karin, Håkon, Magdalena and Eve (me)

---

• Prepare next meeting with the rest of the results also available, incl also snps and continue the report

---

• completness assemblies and haplosemblies - improvement
• detection and counting genes, would be nice also if fragmentation - can we see how many are single / duplicates
• can be use also to compare haplopurge track effect - to adjust purge level - did we do right ? eg comparison before and after purging -> can we see simple and duplicated ?

Possible solutions to read

• https://academic.oup.com/nargab/article/2/2/lqaa026/5836691?login=false

• sorting out : differences alleles vs parallogs ?
  maybe clustering and set thresholds of similarities ? vsearch (also some genes might be repeated - so "polyploidy effect?" ... not sure ... deal whith that when its comming)

---

Also :
Kraken detection contamination (eg if use in assemblies)

• importance database
• can increase size kmer
• play with confidence level

Recheck bwa mem info to be sure

• https://www.biostars.org/p/304614/

--- Suggestion genome diploid to be able to have pipeline test for comparison:
Tapeworm genome size: Small genome size (169 Mb) and lack of haploid variation (1 SNP/3.2 Mb) contributed to exceptionally high contiguity with only 85 gaps remaining in regions of low complexity sequence

[evezeyl]

Thomas also suggested this
Phasing ...

• https://www.biorxiv.org/content/10.1101/2024.05.18.594796v1