Provided by: nanofilt_2.8.0-1_all ![bug](/img/bug.png)
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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.