filtlong - quality filtering tool for Nanopore and PacBio reads

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

filtlong 0.2.0                                    January 2019                                       FILTLONG(1)

       filtlong - quality filtering tool for Nanopore and PacBio reads

positionalarguments:
       input_reads
              input long reads to be filtered

   optionalarguments:
              output thresholds:

       -t[int], --target_bases [int]
              keep only the best reads up to this many total bases

       -p[float], --keep_percent [float]
              keep only this percentage of the best reads (measured by bases)

       --min_length [int]
              minimum length threshold

       --min_mean_q [float]
              minimum mean quality threshold

       --min_window_q [float]
              minimum window quality threshold

              external  references (if provided, read quality will be determined using these instead of from the
              Phred scores):

       -a[file], --assembly [file]
              reference assembly in FASTA format

       -1[file], --illumina_1 [file]
              reference Illumina reads in FASTQ format

       -2[file], --illumina_2 [file]
              reference Illumina reads in FASTQ format

              score weights (control the relative contribution of each score to the final read score):

       --length_weight [float]
              weight given to the length score (default: 1)

       --mean_q_weight [float]
              weight given to the mean quality score (default: 1)

       --window_q_weight [float]
              weight given to the window quality score (default: 1)

              read manipulation:

       --trim trim non-k-mer-matching bases from start/end of reads

       --split [split]
              split reads at this many (or more) consecutive non-k-mer-matching bases

              other:

       --window_size [int]
              size of sliding window used when measuring window quality (default: 250)

       --verbose
              verbose output to stderr with info for each read

       --version
              display the program version and quit

       -h, --help
              display this help menu

       For more information, go to: https://github.com/rrwick/Filtlong

filtlong {OPTIONS} [input_reads]