sand_align_kernel(1)

💖 sand_align_kernel — the manual, but make it make sense 💖

okay bestie, sit down, hydrate, and let me tell you about sand_align_kernel from the Cooperative Computing Tools. it's giving "align candidate sequences sequentially" and honestly? it's lowkey iconic. ✨

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✨ NAME ✨

sand_align_kernel — align candidate sequences sequentially 🧬💅

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🌸 SYNOPSIS 🌸

sand_align_kernel [options] [input file]

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🦋 DESCRIPTION 🦋

so like, sand_align_kernel aligns candidate sequences sequentially. that's the whole vibe.

ngl, you're not normally the one calling this — it's not a "you" program, it's a "the system" program. it gets invoked by sand_align_master(1) for each sequential step of a distributed alignment workload. main character energy but backstage, yk? 🎭

the options you hand to sand_align_kernel control the type of alignment (Smith-Waterman, Prefix-Suffix, Banded, etc.) and the quality threshold for reporting alignments. and how do those options get in there? bestie, they're typically passed in by giving the -e option to sand_align_master. periodt.

now, sand_align_kernel reads a list of sequences from the given input file, or from standard input if you don't give it one. no file? no problem, it'll just take it from stdin like a chill little gremlin. 🙈

the sequences are in the compressed fasta format produced by sand_compress_reads(1). ok and here's the tea on how it actually compares them:

• the first sequence in the input is compared against all following sequences until a separator line.
• following that separator, the next sequence is compared against all following sequences until the following separator.
• and so on. forever and ever. slay. 💫

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💅 OPTIONS 💅

• -a <sw|ps|banded> — specify the type of alignment: sw (Smith-Waterman), ps (Prefix-Suffix), or banded. if you don't say anything, the default is banded. pick your fighter.
• -o <ovl|ovl_new|align|matrix> — specify how each alignment should be output: ovl (Celera V5, V6 OVL format), ovl_new (Celera V7 overlap format), align (display the sequences and alignment graphically) or matrix (display the dynamic programming matrix). sand_align_master(1) expects the ovl output format, which is the default. the other formats are useful for debugging. 🐛✨
• -m <length> — minimum alignment length (default: 0). short alignments stay in their lane.
• -q <quality> — minimum match quality (default: 1.00).
• -x — delete input file after completion. it said "you're done here" and meant it. 💀
• -d <subsystem> — enable debugging for this subsystem. (try -d all to start.)
• -v — show program version. gotta know what era we're in. 👑
• -h — display this message. hi, hello, here's your help. 🫶

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🌈 EXIT STATUS 🌈

• on success, returns zero. 💚
• on failure, returns non-zero. 😭

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⭐ EXAMPLES ⭐

fr fr, users do not normally invoke sand_align_kernel directly. instead, pass arguments by using the -e option to sand_align_master(1). no cap.

for example, to specify a minimum alignment length of 5 and a minimum quality of 0.25:

% sand_align_master sand_align_kernel -e "-m 5 -q 0.25" mydata.cand mydata.cfa mydata.ovl

ate. no crumbs. 🔥

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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.

yes bestie, that's the legal bit, it stays exactly as it is. 💜

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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 page, bestie. this was CCTools 8.0.0 DEVELOPMENT, and yeah, that's the version AND the date situation — go off, kernel. stay aligned, stay gorgeous. 💖✨🦋🌸💅