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I've tried herro on one of our read sets (with R9.4.1 model) and when I compare the reads before and after correction, by aligning them on the reference assembly, the result is very convincing (very few INDEL errors left.) But when I assemble the reads with hifiasm 0.19.8 I lose close to all reads (95%) during the first hifiasm correction step : comparing first and second kmer histograms in hifiasm logs. This is not the case when I assemble HiFi reads.
Which hifiasm options should I change to limit this phenomenon?
The text was updated successfully, but these errors were encountered:
After after a second check the drop in kmer coverage is also found with HiFi reads. Still I do not understand why the assembly metrics are so low : hifiasm is using a very low number of reads for the assembly, this can be seen in the gfa coverage values
I've tried herro on one of our read sets (with R9.4.1 model) and when I compare the reads before and after correction, by aligning them on the reference assembly, the result is very convincing (very few INDEL errors left.) But when I assemble the reads with hifiasm 0.19.8 I lose close to all reads (95%) during the first hifiasm correction step : comparing first and second kmer histograms in hifiasm logs. This is not the case when I assemble HiFi reads.
Which hifiasm options should I change to limit this phenomenon?
The text was updated successfully, but these errors were encountered: