NAME

       NanoFilt - filtering and trimming of long read sequencing data

DESCRIPTION

       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

SEE ALSO

       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

              info NanoFilt

       should give you access to the complete manual.

NanoFilt 2.6.0                                      June 2020                                        NANOFILT(1)