alignpairedend score threshold
The alignment scores computed by alignpairedend are not equivalent to those computed by the OBITools1's illuminapairedend as the alignment method is different.
The threshold value of 40 commonly used in OBITools1 pipelines and determined empirically for the OBITools1 does not apply to the OBITools3 and the equivalent threshold value should be determined.
To upload designs, you'll need to enable LFS and have an admin enable hashed storage. More information