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Hi,

I seek help understanding the final output. I have processed a file with around 2000 sequences, with the objective of locating a SNP in a 10 nucleotide region. The software was perfect to locate this SNP, however it seems some reads which spanned this region have been dropped during the analysis. Attached I send two of the output files the pos.txt has the correct number of reads, however in the hap.txt these are reduced and for the read.txt this is the same. I would like to understand why this is happening.

Thanks in advanced.

Hi, can there be more than 1 contig in the fasta file input if I specify the contig name in the bed file?
Thanks.

Dear,

First of all, sorry for asking about nanopore in the first issue when it is clearly indicated that this pipeline is ment for PacBio HiFi reads.

BUT, since it takes as input the assembly and the BAM file, I guess it could run also with an assembly and alignment file created using nanopore reads. So, my question is, do you expect similar efficiency at separating haplotypes within MAGs? Because, a priori, the biggest difference is the lower accuracy of nanopore reads.

As you can imagine, I have some MAGs in my dataset generated using nanopore's long read sequencing and it would be nice to test your approach on these.

Regards,
Cristian