Hello, I am looking for SNPs in the rDNA of fungal genomes.
I have a consensus sequence (~100 bps), and a lot of reads taken from a WGS (~900 bps) that align to it, the reads are provided together with their quality scores.
I'd like to look for SNPs among these reads, is there a software ready to use or should I write one by myself? I have seen MAQ, but it seems it works only with short reads. Do you have any suggestions?
thank you
I have a consensus sequence (~100 bps), and a lot of reads taken from a WGS (~900 bps) that align to it, the reads are provided together with their quality scores.
I'd like to look for SNPs among these reads, is there a software ready to use or should I write one by myself? I have seen MAQ, but it seems it works only with short reads. Do you have any suggestions?
thank you
Comment