NANOOK(1)

✨ NAME ✨

nanook — the flexible, multi-reference software for pre- and post-alignment analysis of nanopore sequencing data, quality and error profiles. 💖

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🦋 SYNOPSIS 🦋

nanook <extract|align|analyse|compare|process> [options]

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🌸 DESCRIPTION 🌸

NanoOK (pronounced na-nook, say it with your whole chest) is a tool for extraction, alignment and analysis of Nanopore reads. 💅

Bestie, here's the tea: NanoOK will extract reads as FASTA or FASTQ files, align them (and yes, you get a choice of alignment tools, we love options), then generate a comprehensive multi-page PDF report containing yield, accuracy and quality analysis. <sparkle>✨</sparkle>

And along the way? It generates plain text files which can be used for further analysis, plus graphs suitable for inclusion in presentations and papers. It's giving main character energy honestly. 👑

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🎀 OPTIONS 🎀

🧚 extract options

• -s, -sample <dir> — specifies sample directory 📁
• -f, -reads — specifies alternative dir for FAST5 files (default fast5)
  • It can be absolute (beginning with /) or relative, e.g. -f reads/downloads if replicating Metrichor file structure. iykyk
• -a, -fasta — specifies FASTA file extraction (default) ⭐
• -q, -fastq — specifies FASTQ file extraction ⭐
• -basecallindex — specifies the index of the analysis (default: latest)
• -mergereads — to generate merged FASTA files in addition to single read files 🫶
• -minquality <value> — to set the minimum quality for a 'pass' read

🧚 align options

• -s, -sample <dir> — specifies sample directory 📁
• -r, -reference <path> — specifies path to reference database
• -aligner <name> — specifies the aligner (default last)
• -alignerparams <params> — specifies parameters to the aligner
• -showaligns — echoes aligner commands to screen 🖥️

🧚 analyse options

• -s, -sample <dir> — specifies sample directory 📁
• -r, -reference <path> — specifies path to reference database
• -aligner <name> — specifies the aligner (default last)
• -coveragebin <int> — specifies coverage bin size (default 100)
• -bitmaps — to output bitmap PNG graphs instead of PDF 🖼️

🧚 compare options

• -l, -samplelist <file> — specifies a sample list file
• -o, -outputdir <directory> — specifies an output directory
• -type <2d|template|complement> — specifies an output directory

not me noticing that -type says "output directory" again 🙈 but fr fr that's literally what the page says, so that's what you get, no cap

🧚 process options

• -process <file> — specifies a process file

🧚 Read type options

• -passonly — to analyse only pass reads
• -failonly — to analyse only fail reads
• -2donly — to analyse only 2D reads
• -templateonly — to analyse just Template reads
• -complementonly — to analyse just Complement reads

🧚 Other options

• -t, -numthreads <number> — specifies the number of threads to use (default 1) 🔥
• -log <filename> — enables debug logging to file
• -force — to force NanoOK to ignore warnings ⚠️ lowkey spicy, tread carefully bestie
• -timeout — to set the number of seconds before giving up waiting for new reads (default 2)

Valid aligners: last, bwa, blasr, marginalign, graphmap 🌈

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💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🎀

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okay that's the whole page bestie, you ate that 💅 this was nanook version 1.26, dated September 2017 — go forth and align, mwah 🫶✨