I am looking for mutations within a population in a particular region in reference to the nucleotide sequence of the same region. Alignment tools like bowtie and BWA require genome assembly. However, I want to align and visualize the sequences obtained against the nucleotide sequence of a gene that I have isolated. Kindly suggest a tool or a pipeline to do so.
Iryna Goraichuk
You can use both Bowtie2 and BWA-MEM (as well as many others like Minimap2, LAST, GraphMap, NanoPipe... ) for the alignment of your data to the reference sequence. I would recommend the Geneious or Qiagen CLC platform. Keep in mind, that you will have to basecall the raw fast5 reads first and then use the data converted to fastq or fasta format for the alignment.
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