Nanopolish "eventalign" command not completing in time limit.

[baibhav-bioinfo]

i am doing nanopolish-eventalign for my nanopore direct RNA sequence reads. I have 9 samples, for a sample the command is running for more than 24 hours and is not able to complete within time limits and getting terminated.

Is there any way i can do the process faster? Can we split the .Fastq files into 4 partitions for each samples. Then we will have 4 eventalign.txt files per sample, can we merge it and then go for "Xpore dataprep" step, or we have to it separately for each part and then merge the results before giving to "diffmod".

I am concerned if my data will loose any biological meaningfulness in the partitioning and merging.

[yuukiiwa]

Hi @baibhav-bioinfo,

You can increase the threads with -t to make it faster. Or if you have GPU, you can checkout https://github.com/hasindu2008/f5c, which is GPU-implementation of nanopolish.

Alternatively, you can also split the fastq.

Thanks!

Best wishes, Yuk Kei