sand_filter_kernel(1)

✨ sand_filter_kernel ✨

okay bestie, welcome to the sand_filter_kernel(1) page 💅 this one lives in the Cooperative Computing Tools manual, and it's literally the little engine that could for sequence filtering 🧚

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🌸 NAME 🌸

sand_filter_kernel — filter read sequences sequentially 💖

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🎀 SYNOPSIS 🎀

sand_filter_kernel [options] <sequence file> [second sequence file]

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🦋 DESCRIPTION 🦋

so sand_filter_kernel filters a list of genomic sequences and spits out a list of candidate pairs, which then go off to get a way more detailed alignment 😌

ngl, you're not normally the one calling this one directly. It gets invoked by sand_filter_master(1) for each sequential step of a distributed alignment workload. It's giving backstage crew, not main character. But it ate, fr fr.

Here's the tea on how it reads your files 👇

• If you give it one sequence file, sand_filter_kernel will look for similarities between all the sequences in that file.
• If you give it two files, it will look for similarities between sequences in the first file and the second file.

And the output? A list of candidate pairs 💖 listing the name of the candidate sequences and a starting position for alignment. iconic behavior honestly.

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✨ OPTIONS ✨

• -s <size> — Size of "rectangle" for filtering. You can determine the size dynamically by passing in d rather than a number. no cap, that d is doing a lot of heavy lifting 🫶
• -r <file> — A meryl file of repeat mers to be ignored. bye bye repeats 💀
• -k <size> — The k-mer size to use in candidate selection (default is 22).
• -w <number> — The minimizer window size to use in candidate selection (default is 22).
• -o <filename> — The output file. Default is stdout. (so if you don't say anything, it just yells into your terminal, love that for it 🌈)
• -d <subsystem> — Enable debug messages for this subsystem. Try -d all to start. 👀
• -v — Show version string.
• -h — Show help screen.

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💀 EXIT STATUS 💀

• On success, returns zero ✨
• On failure, returns non-zero 😭

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🌈 EXAMPLES 🌈

okay so real talk: users do not normally invoke sand_filter_kernel directly. Instead, options such as the k-mer size, minimizer window, and repeat file may be specified by the same arguments to sand_filter_master(1) instead. it's giving "don't talk to the kernel, talk to the master" 😌

For example, to run a filter with a k-mer size of 20, window size of 24, and repeat file of mydata.repeats:

% sand_filter_master -k 20 -w 24 -r mydata.repeats mydata.cfa mydata.cand

periodt. 💅

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👑 COPYRIGHT 👑

The Cooperative Computing Tools are Copyright (C) 2005-2019 The University of Notre Dame. This software is distributed under the GNU General Public License. See the file COPYING for details.

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🫶 SEE ALSO 🫶

• Cooperative Computing Tools Documentation
• SAND User Manual
• sand_filter_master(1) sand_filter_kernel(1) sand_align_master(1) sand_align_kernel(1) sand_compress_reads(1) sand_uncompress_reads(1) work_queue_worker(1)

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and that's the whole vibe check bestie 🧚 this page was brought to you by CCTools 8.0.0 DEVELOPMENT, serving the Cooperative Computing Tools manual, and yes it's still out here being sand_filter_kernel(1) at the bottom of every page like the little signature it is 💖 go read sand_filter_master(1) next, iykyk 🌸