NanoFilt - filtering and trimming of long read sequencing data

       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.

   Generaloptions:-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

   Optionsforfilteringreadson.:-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.

   Optionsfortrimmingreads.:--headcrop HEADCROP
              Trim n nucleotides from start of read

       --tailcrop TAILCROP
              Trim n nucleotides from end of read

   Inputoptions.:-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

       NanoFilt - filtering and trimming of long read sequencing data

       The full documentation for NanoFilt is maintained as a Texinfo manual.  If the info and NanoFilt programs
       are properly installed at your site, the command

              infoNanoFilt

       should give you access to the complete manual.

NanoFilt 2.6.0                                      June 2020                                        NANOFILT(1)