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
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