FAST5_TO_SEQ_SUMMARY(1)

Okay bestie, this is the FAST5_TO_SEQ_SUMMARY(1) manual from User Commands, and it's giving practical 💅✨

✨ NAME ✨

Fast5_to_seq_summary, generate a sequencing summary like file from a directory containing Fast5 files 🧚

💖 DESCRIPTION 💖

Here's the usage line, so you know what you're typing 🎀

usage: Fast5_to_seq_summary [-h] [--version] --fast5_dir FAST5_DIR

--seq_summary_fn SEQ_SUMMARY_FN
[--max_fast5 MAX_FAST5] [--threads THREADS] [--basecall_id
BASECALL_ID] [--fields FIELDS [FIELDS ...]] [--include_path]
[--verbose_level VERBOSE_LEVEL]

Lowkey the whole point is that Fast5_to_seq_summary takes a directory full of Fast5 files and generates a sequencing summary-like file from them 🦋 No cap, that's the entire main character energy of this tool 👑

🎀 optional arguments 🎀

• -h, --help — the "help me" button 🙈 It shows this help message and exits.
• --version, -v — shows the program's version number and then exits 🔥
• --fast5_dir FAST5_DIR, -f FAST5_DIR — the directory holding your fast5 files 📂 It can have multiple subdirectories too, so don't stress.
• --seq_summary_fn SEQ_SUMMARY_FN, -s SEQ_SUMMARY_FN — the path to the sequencing summary file where all the data pulled from the fast5 files gets written 📝
• --max_fast5 MAX_FAST5 — the max number of files to try parsing 🌸 0 deactivates the limit (default: 0)
• --threads THREADS, -t THREADS — the total number of threads you want 🧵 One is for the reader and one is for the writer, so the minimum is 3 bestie (default: 4)
• --basecall_id BASECALL_ID — the id of the basecalling group 🍓 It's 0 unless you change it. But if you run multiple basecalling passes on the same fast5 files, use this to label each group (1, 2 ...) (default: 0)
• --fields FIELDS [FIELDS ...] — the list of field names for the attributes you want to try grabbing from the fast5 files ✨ (default: ['read_id', 'run_id', 'channel', 'start_time', 'sequence_length_template', 'mean_qscore_template', 'calibration_strand_genome_template', 'barcode_arrangement'])
• --include_path — if you add this, the absolute path to the matching file gets tossed into an extra column 🗺️ (default: False)
• --verbose_level VERBOSE_LEVEL — how chatty it gets, from 2 (Chatty) all the way down to 0 (Nothing) 🤫 (default: 0)

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🫶 AUTHOR 🫶

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. Iconic behavior, honestly 💜

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Okay that's the whole tea, bestie 🌈 Fast5_to_seq_summary version 2.5.2, last updated December 2020. Stay iconic and go make your summary files 💖✨