usage: filtlong {OPTIONS} [input_reads]

Filtlong: a quality filtering tool for Nanopore and PacBio reads

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
      --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

      --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: