AptaSelect

AptaSelect identifies high-frequency aptamer candidate sequences from paired-end SELEX FASTQ files. Each read (R1 and R2 separately) is filtered in three stages: approximate (edit-distance) matching of both constant regions on either strand, exact-marker flanking extraction, and exact-stem random-region extraction at a user-set length. Identical sequences at every stage are counted and stably ranked by frequency. All library-design sequences, tolerances and lengths are configurable. Reads are processed by multiple worker processes with results merged in original read order; Stage 1 uses the compiled edlib edit-distance library behind an exact-piece (pigeonhole) prefilter. Motif add-on: the top-count random-region cores (a fixed number or a top percentage of the ranked list) are always written to a FASTA file, and MEME (DNA alphabet, serial mode, off by default) can be run on them to find shared motifs, with results in meme_out/. The count-sorting outputs are unchanged from version 1.0.1.