You must specify an input file of a directory path to a set of input files. kmer_filter 1.35 kmer_filter [-f in_file_1 [-f in_file_2...] | -p in_dir] [-1 pair_1 -2 pair_2 [-1 pair_1...]] -o out_dir [-i type] [-y type] [-D] [-h] f: path to the input file if processing single-end seqeunces. i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). p: path to a directory of files (for single-end files only). 1: specify the first in a pair of files to be processed together. 2: specify the second in a pair of files to be processed together. o: path to output the processed files. y: output type, either 'fastq' or 'fasta' (default fastq). D: capture discarded reads to a file. h: display this help messsage. Filtering options: --rare: turn on filtering based on rare k-mers. --abundant: turn on filtering based on abundant k-mers. --k_len : specify k-mer size (default 15). Advanced filtering options: --max_k_freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). --min_lim : specify number of rare kmers occuring in a row required to discard a read (default 80% of the k-mer length). --max_lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). Normalize data: --normalize : normalize read depth according to k-mer coverage. Characterizing K-mers: --write_k_freq: write kmers along with their frequency of occurrence and exit. --k_dist: print k-mer frequency distribution and exit. Advanced input options: --read_k_freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files.