FILTERS(1)

💖 FILTERS(1) — the overlap glow-up page 💖

okay bestie, gather round, because this is the manual page for Filters, a low quality overlap filtering tool, and it lives in section 1 of the manual (User Commands energy). no cap. 🦋

✨ NAME ✨

Filters — low quality overlap filtering. that's it, that's the name, and it does exactly what it says on the tin. 🎀

🌸 SYNOPSIS 🌸

fsa_ol_filter [options] overlaps filtered_overlaps

💅 DESCRIPTION 💅

it's a command line tool, and its whole job is to filter out low-quality overlaps prior to assembling. like, it's the bouncer at the club door of your assembly, checking IDs and telling the messy ones to go home. 🔥

this takes the following parameters:

• overlaps — the input filename 📥
• filtered_overlaps — the resulting ouput filename (yes "ouput", that's literally what the page says, we are not fixing it, it's part of the lore 🙈)

👑 OPTIONS 👑

one bullet per flag, all defaults included, no skipping, periodt.

• --min_length=INT — minimum length of reads. default: 2500
• --max_length=INT — maximum length of reads. default: 2147483647
• --min_identity=DOUBLE — minimum identity of overlaps. default: 90
• --min_aligned_length=INT — minimum aligned length of overlaps. default: 2500
• --max_overhang=INT — maximum overhang of overlaps. a negative number = determined by the program. default: 10
• --min_coverage=INT — minimum base coverage. a negative number = determined by the program. default: -1
• --max_coverage=INT — maximum base coverage. a negative number = determined by the program. default: -1
• --max_diff_coverage=INT — maximum difference of base coverage. a negative number = determined by the program. default: -1
• --coverage_discard=DOUBLE — discard ratio of base coverage. if max_coverage or max_diff_coverage is negative, it will be reset to (100-coverage_discard)th percentile. default: 0.01
• --overlap_file_type="|m4|m4a|paf|ovl" — overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON. default: ""
• --bestn=INT — output best n overlaps on 5' or 3' end for each read. default: 10
• --genome_size=INT — genome size. it determines the maximum length of reads with coverage together. default: 0
• --coverage=INT — coverage. it determines the maximum length of reads with genome_size together. default: 0
• --output_directory=STRING — directory for output files. default: "."
• --thread_size=INT — number of threads. default: 4

🫶 the encore (yes, the page really does this twice) 🫶

not me reading the source page and finding the whole thing again, bestie. the original literally repeats itself, so here it is again, every single line, because the one rule is we keep every detail. 💀

Usage: fsa_ol_filter [options] overlaps filtered_overlaps

• overlaps — input filename
• filtered_overlaps — ouput filename
• --min_length=INT — minimum length of reads. default: 2500
• --max_length=INT — maximum length of reads. default: 2147483647
• --min_identity=DOUBLE — minimum identity of overlaps. default: 90
• --min_aligned_length=INT — minimum aligned length of overlaps. default: 2500
• --max_overhang=INT — maximum overhang of overlaps. a negative number = determined by the program. default: 10
• --min_coverage=INT — minimum base coverage. a negative number = determined by the program. default: -1
• --max_coverage=INT — maximum base coverage. a negative number = determined by the program. default: -1
• --max_diff_coverage=INT — maximum difference of base coverage. a negative number = determined by the program. default: -1
• --coverage_discard=DOUBLE — discard ratio of base coverage. if max_coverage or max_diff_coverage is negative, it will be reset to (100-coverage_discard)th percentile. default: 0.01
• --overlap_file_type="|m4|m4a|paf|ovl" — overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON. default: ""
• --bestn=INT — output best n overlaps on 5' or 3' end for each read. default: 10
• --genome_size=INT — genome size. it determines the maximum length of reads with coverage together. default: 0
• --coverage=INT — coverage. it determines the maximum length of reads with genome_size together. default: 0
• --output_directory=STRING — directory for output files. default: "."
• --thread_size=INT — number of threads. default: 4

and that's the whole menu, twice, because the page said so and we do not argue with the page. 🌈

🌟 bye bestie 🌟

the footer of this page says "Filters out low-quality overlap..." and it's dated July 2020, and it signs off as FILTERS(1). so that's the vibe, that's the version, that's the date — iconic, frozen in time, main character energy. go filter those overlaps. slay. 💖✨🎀🦋🌸💅🫶😭🔥👑🌈⭐💀🙈🍓🧚💜