Program options for NanoFilt: 

usage: NanoFilt [-h] [-v] [--logfile LOGFILE] [-l LENGTH]
                [--maxlength MAXLENGTH] [-q QUALITY] [--minGC MINGC]
                [--maxGC MAXGC] [--headcrop HEADCROP] [--tailcrop TAILCROP]
                [-s SUMMARY] [--readtype {1D,2D,1D2}]
                [input]

Perform quality and/or length and/or GC filtering of (long read) fastq data.           Reads on stdin.

General options:
  -h, --help            show the help and exit
  -v, --version         Print version and exit.
  --logfile LOGFILE     Specify the path and filename for the log file.
  input                 input, uncompressed fastq file

Options for filtering reads on.:
  -l LENGTH, --length LENGTH
                        Filter on a minimum read length
  --maxlength MAXLENGTH
                        Filter on a maximum read length
  -q QUALITY, --quality QUALITY
                        Filter on a minimum average read quality score
  --minGC MINGC         Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if
                        using summary file.
  --maxGC MAXGC         Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if
                        using summary file.

Options for trimming reads.:
  --headcrop HEADCROP   Trim n nucleotides from start of read
  --tailcrop TAILCROP   Trim n nucleotides from end of read

Input options.:
  -s SUMMARY, --summary SUMMARY
                        Use albacore or guppy summary file for quality scores
  --readtype {1D,2D,1D2}
                        Which read type to extract information about from summary. Options are 1D, 2D or
                        1D2

EXAMPLES:
  gunzip -c reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | minimap2 genome.fa - | samtools sort -O BAM -@24 -o alignment.bam -
  gunzip -c reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | gzip > trimmed-reads.fastq.gz
  gunzip -c reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz


----------------------------------------------