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LuoGroup2023 / DeChat

Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat
GNU General Public License v3.0
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R9.4 #2

Open chklopp opened 3 months ago

chklopp commented 3 months ago

Hi,

Is it possible to correct R9.4 reads with DeChat? If yes, which parameters should we use?

LuoGroup2023 commented 3 months ago

Hi,

Is it possible to correct R9.4 reads with DeChat? If yes, which parameters should we use?

Hi,

I apologize for the inconvenience. In our initial testing phase, the error correction performance for our own R9.4 reads was not particularly satisfactory. However, if your data error rate is within 3.5%, you can still try using DeChat for error correction, as it can still provide a decent error correction performance.

For reads with higher error rates, we recommend increasing the number of rounds of MSA (Multiple Sequence Alignment), typically to 6-9 rounds. Additionally, consider setting the maximum allowed error rate used for filtering overlaps higher, perhaps to 0.06.

Best regards,

Yichen