DEEPNANO_BASECALL(1)

💖 DEEPNANO_BASECALL(1) 💖

okay bestie, pull up a chair, we're talking about deepnano_basecall from the DEEPNANO_BASECALL(1) manual, and honestly? she's iconic. she's a basecaller for Oxford Nanopore MinION reads based on deep recurrent neural networks. yes, recurrent, yes, deep, yes she's that girl. 🧠✨

✨ SYNOPSIS ✨

usage: deepnano_basecall [ARGS] [reads [reads ...]]

🌸 DESCRIPTION 🌸

🌈 positional arguments:

• reads — the reads, babes. that's it, that's the vibe.

🎀 optional arguments:

• -h, --help — shows this help message and dips out. classic. exit stage left. 👋
• --template_net TEMPLATE_NET — the path to the network that basecalls the template. she comes with a reasonable default already, so no pressure. 💅
• --complement_net COMPLEMENT_NET — the path to the network that basecalls the complement. also has a reasonable default, we stay prepared. 🫶
• --big_net BIG_NET — path to the network that basecalls 2D. and yes, she has a reasonable default too. ✨
• --timing — if you set this, she'll display timing information for each read. nosy in the best way. ⏱️
• --type TYPE — pick your fighter: one of template, complement, 2d, all. use a comma to separate multiple options, eg.: template,complement. this is the type of basecalling output, and it defaults to all. main character energy, honestly. 👑
• --output OUTPUT — output filename. give her a name bestie. 📝
• --output_orig — if set, she also outputs Metrichor basecalls. bonus content, we love a little extra. 🍓
• --directory DIRECTORY — the directory where the read files are stored. show her where the goods live. 📂

🔥 EXAMPLES 🔥

for SQK-MAP-006 chemistry, just use this, no cap:

OMP_NUM_THREADS=1 deepnano_basecall <list of fast5 files>

or, if you're feeling that other vibe:

OMP_NUM_THREADS=1 deepnano_basecall --directory <directory with reads>

she outputs basecalls for template, complement and 2D into a file named output.fasta. periodt. 💖

for SQK-MAP-005 chemistry, use this instead:

OMP_NUM_THREADS=1 deepnano_basecall --template_net nets_data/map5temp.npz --complement_net nets_data/map5comp.npz --big_net nets_data/map5-2d.npz <list of fast5 files>

🦋 SEE ALSO 🦋

deepnano_basecall_no_metrichor(1) — go say hi to her sister. 💜

👑 AUTHOR 👑

This manpage was written by Çağrı ULAŞ for the Debian distribution and can be used for any other usage of the program. thank you for your service, legend. 🫡

💀 BUGS 💀

Report bugs to <https://bitbucket.org/vboza/deepnano/issues> — she wants to hear from you, fr fr. don't be shy. 🙈

okay that's the whole page!! this was deepnano_basecall version 0.0+20110617, dated February 2017, and honestly she ate and left no crumbs. slay, bestie, go basecall something iconic. 🌈⭐💅