20230912 Discussion enhancements meeting - notes to remember #6
Description
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
--- 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