NANOSTAT(1)

✨ NANOSTAT(1) ✨

Hey bestie, this is the NanoStat page from the User Commands section 💖 Let's get into it 🦋

🌸 NAME 🌸

NanoStat is the one and only manual page for NanoStat 1.4.0 🧚

💜 DESCRIPTION 💜

Okay so here's the usage line you need to know 👀

usage: NanoStat [-h] [-v] [-o OUTDIR] [-p PREFIX] [-n NAME] [-t N]
[--tsv]

       [--barcoded] [--readtype {1D,2D,1D2}] (--fastq file [file ...] |
       --fasta file [file ...] | --summary file [file ...] | --bam file
       [file ...] | --ubam file [file ...] | --cram file [file ...] |
       --feather file [file ...])

NanoStat is all about calculating statistics for a long read sequencing dataset. It's giving data scientist realness 📊✨

🎀 General options

• -h, --help — pulls up the help and then exits, no drama 💅
• -v, --version — prints the version and exits 🌈
• -o, --outdir OUTDIR — picks a directory for the output, but only works when you also use -n 📁
• -p, --prefix PREFIX — adds an optional prefix to the output file 🎀
• -n, --name NAME — sets a filename or path for the output. If you don't pick one, it goes to stdout by default 🖨️
• -t, --threads N — sets how many threads the script is allowed to use 🧵
• --tsv — outputs the stats as a properly formatted TSV 🍓

🦋 Input options.

• --barcoded — use this if you want to split the summary file by barcode 🧩
• --readtype {1D,2D,1D2} — tells it which read type to pull info about from the summary. Your choices are 1D, 2D, and 1D2 💖

🫧 Input data sources, one of these is required.

Bestie, you need to pick at least one of these 🫶

• --fastq file [file ...] — your data lives in one or more (compressed) fastq files 🧃
• --fasta file [file ...] — your data lives in one or more (compressed) fasta files 🍬
• --summary file [file ...] — your data lives in one or more (compressed) summary files generated by albacore or guppy 🧪
• --bam file [file ...] — your data lives in one or more sorted bam files 🗂️
• --ubam file [file ...] — your data lives in one or more unmapped bam files 🫥
• --cram file [file ...] — your data lives in one or more sorted cram files 🌙
• --feather file [file ...] — your data lives in one or more feather files 🪶

🧁 EXAMPLES:

Here's how you can slay with it 💅

NanoStat --fastq reads.fastq.gz --outdir statreports NanoStat
--summary sequencing_summary1.txt
sequencing_summary2.txtsequencing_summary3.txt --readtype 1D2
NanoStat --bam alignment.bam alignment2.bam

🦋 SEE ALSO 🦋

Okay so the full documentation for NanoStat is maintained as a Texinfo manual 📚 If the info and NanoStat programs are properly installed at your site, run this command and you'll get the complete manual:

info NanoStat

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That's the tea, bestie 🫶 You've been reading NanoStat 1.4.0 from December 2020, filed under NANOSTAT(1) 💖✨