table of contents
NANOFILT(1) | User Commands | NANOFILT(1) |
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.
June 2020 | NanoFilt 2.6.0 |