Allows paired or single-end reads to be filtered according to the number or rare or abundant kmers they contain. Useful for both RAD datasets as well as randomly sheared genomic or transcriptomic data.

Program Options

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]

Filtering options:

Advanced filtering options:

Normalize data:

Characterizing K-mers:

Advanced input options:

Example Usage

% kmer_filter

Other Pipeline Programs

Raw Reads


Execution control