NAME

       filtlong - quality filtering tool for Nanopore and PacBio reads

SYNOPSIS

       filtlong {OPTIONS} [input_reads]

OPTIONS

   positional arguments:
       input_reads
              input long reads to be filtered

   optional arguments:
              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

AUTHOR

       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)