I am looking to align a fastq file of 50mer sequences against a reference genome. I am looking to return ALL possible alignments, not just the best alignments. I looked at using Bowtie2 with the -a flag, however in the documenation it says "Some tools are designed with this reporting mode in mind. Bowtie 2 is not! For very large genomes, this mode is very slow.".
Which tools are designed with this in mind? Ideally the output would return alignments in descending order by alignment score, equivalent to Bowtie2. If there is not a better option for this workflow, I will stick to using Bowtie2. Thanks in advance.