JiaoLaboratory

it seems some errors in craq running. by the way, could you check is the Output/LRout/LR_sort.bam and LR_sort.depth normally generated or is empty? if not, maybe CRAQ run disturbed by...

Thank you for using CRAQ. Yes, this is reasonable. If several error sites are very close to each other, such as clustered within a 10k window, these errors likely originate...

Thank you. Unfortunately, CRAQ currently does not include a user-defined parameter for clustering error hotspots, which requires users to manually process the out_srfilter_CSE.out file according to their needs. Additionally, empirically,...

Thank you for using CRAQ! CRAQ also supports second-generation sequencing BAM files generated using BWA alignment, so this will not affect the analysis results.

Apologies for the late response. Both single long reads (PacBio/Nanopore) and hybrid approaches combining long and short reads (e.g., Illumina) are acceptable for CRAQ. While the latter （combining long and...

Really great! Thank you for your feedback. I will use it to make improvements.