.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH NANOFILT "1" "June 2020" "NanoFilt 2.6.0" "User Commands"
.SH NAME
NanoFilt \- filtering and trimming of long read sequencing data
.SH DESCRIPTION
usage: NanoFilt [\-h] [\-v] [\-\-logfile LOGFILE] [\-l LENGTH]
.IP
[\-\-maxlength MAXLENGTH] [\-q QUALITY] [\-\-minGC MINGC]
[\-\-maxGC MAXGC] [\-\-headcrop HEADCROP] [\-\-tailcrop TAILCROP]
[\-s SUMMARY] [\-\-readtype {1D,2D,1D2}]
[input]
.PP
Perform quality and/or length and/or GC filtering of (long read) fastq data.           Reads on stdin.
.SS "General options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show the help and exit
.TP
\fB\-v\fR, \fB\-\-version\fR
Print version and exit.
.TP
\fB\-\-logfile\fR LOGFILE
Specify the path and filename for the log file.
.TP
input
input, uncompressed fastq file
.SS "Options for filtering reads on.:"
.TP
\fB\-l\fR LENGTH, \fB\-\-length\fR LENGTH
Filter on a minimum read length
.TP
\fB\-\-maxlength\fR MAXLENGTH
Filter on a maximum read length
.TP
\fB\-q\fR QUALITY, \fB\-\-quality\fR QUALITY
Filter on a minimum average read quality score
.TP
\fB\-\-minGC\fR MINGC
Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if
using summary file.
.TP
\fB\-\-maxGC\fR MAXGC
Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if
using summary file.
.SS "Options for trimming reads.:"
.TP
\fB\-\-headcrop\fR HEADCROP
Trim n nucleotides from start of read
.TP
\fB\-\-tailcrop\fR TAILCROP
Trim n nucleotides from end of read
.SS "Input options.:"
.TP
\fB\-s\fR SUMMARY, \fB\-\-summary\fR SUMMARY
Use albacore or guppy summary file for quality scores
.TP
\fB\-\-readtype\fR {1D,2D,1D2}
Which read type to extract information about from summary. Options are 1D, 2D or
1D2
.SS "EXAMPLES:"
.IP
gunzip \fB\-c\fR reads.fastq.gz | NanoFilt \fB\-q\fR 10 \fB\-l\fR 500 \fB\-\-headcrop\fR 50 | minimap2 genome.fa \- | samtools sort \fB\-O\fR BAM \-@24 \fB\-o\fR alignment.bam \-
gunzip \fB\-c\fR reads.fastq.gz | NanoFilt \fB\-q\fR 12 \fB\-\-headcrop\fR 75 | gzip > trimmed\-reads.fastq.gz
gunzip \fB\-c\fR reads.fastq.gz | NanoFilt \fB\-q\fR 10 | gzip > highQuality\-reads.fastq.gz
.SH "SEE ALSO"
The full documentation for
.B NanoFilt
is maintained as a Texinfo manual.  If the
.B info
and
.B NanoFilt
programs are properly installed at your site, the command
.IP
.B info NanoFilt
.PP
should give you access to the complete manual.