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