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.