Hi there! I have many
.fq files contained long reads (I got them with ONT MiniON). Also I have a
.fasta file contains a specific short sequence (exon from different organism). I want to get if this short sequence aligns against these long reads (is there orthology between organisms?). I do not know what aligner to use, I used to work with short reads and usually I aligned them against a large reference genome (with bwa mem e.g.). In the beginning I do not want to assemble .fastq files. Thanks in advance!