NANOFILT(1)

💖 NanoFilt 💖

Okay bestie, this is the manual page for NanoFilt, filed under User Commands in section 1 🎀 Let's get into it.

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✨ NAME ✨

NanoFilt is the tool for filtering and trimming long read sequencing data 🧬💅

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🌸 DESCRIPTION 🌸

Here's the usage line you'll see when you run it, so you know what the shape of the command looks like 👀

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]

NanoFilt can do quality, length, and/or GC filtering on (long read) fastq data, and it's giving main character energy because it reads from stdin 🦋

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🎀 General options: 🎀

• -h, --help — shows you the help and then exits 🙈
• -v, --version — prints the version and exits ✨
• --logfile LOGFILE — lets you pick the path and filename for the log file 📝
• input — the input, which is an uncompressed fastq file 📁

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💜 Options for filtering reads on.: 💜

• -l LENGTH, --length LENGTH — filters on a minimum read length 📏
• --maxlength MAXLENGTH — filters on a maximum read length 📐
• -q QUALITY, --quality QUALITY — filters on a minimum average read quality score 👑
• --minGC MINGC — the sequences need GC content that's >= this number. It's a float between 0.0 and 1.0. Heads up, this one gets ignored if you're using a summary file 🙈
• --maxGC MAXGC — the sequences need GC content that's <= this number. It's a float between 0.0 and 1.0. Same deal, it gets ignored if you're using a summary file 🙈

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🦋 Options for trimming reads.: 🦋

• --headcrop HEADCROP — trims n nucleotides off the start of the read ✂️
• --tailcrop TAILCROP — trims n nucleotides off the end of the read ✂️

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🧚 Input options.: 🧚

• -s SUMMARY, --summary SUMMARY — uses an albacore or guppy summary file to get the quality scores 🍓
• --readtype {1D,2D,1D2} — picks which read type to pull info about from the summary. Your choices are 1D, 2D, or 1D2 🌈

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💅 EXAMPLES: 💅

Here are some looks you can copy. Slay 🔥

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

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🫶 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 below should give you access to the complete manual 📚

info NanoFilt

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Bestie, that's the whole page 💖 NanoFilt 2.6.0 from June 2020, filed under NANOFILT(1). Stay iconic 🌈💅✨