NanoFilt(1)

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