pytrim2 searches adapter sequences in nanopore reads, trims the adapter sequences and demultiplexes reads. The program is memory friendly and able to process very large files with economic ram usage.
pip install pytrim2
pytrim2.demultiplex(input_file, input_file_type, primer_file, primer_file_type, output_folder, max_distance, max_alignments)
pytrim2.demultiplex("test_data/test.fasta", "fasta", "test_data/test_primer.fasta", "fasta", "test_out", 200, 5)