FSA_CTG_BRIDGE(1)

💅 fsa_ctg_bridge(1) — the manual page, but make it make sense

okay so bestie, welcome to fsa_ctg_bridge, a User Command, and I'm gonna hold your hand through every single line of this thing. it's giving "bioinformatics but make it cute". no cap. 🧬✨

🌸 NAME 🌸

fsa_ctg_bridge — bridge contigs. that's it. that's the whole job. it bridges contigs. iconic behaviour honestly. 🫶

✨ SYNOPSIS ✨

fsa_ctg_bridge [options] rawreads contigs read2ctg bridged_contigs

four positional arguments, no skipping, we love a structured queen. 👑

💖 DESCRIPTION 💖

so like, this is a command line tool to bridge contigs. periodt. 💅

it takes the following parameters, and yes you have to give it all of them:

• rawreads — the rawread file 📖
• contigs — the contig file 🧵
• read2ctg — the file containing overlaps between rawread and contigs 🔗
• bridged_contigs — the output file 🎀 (this is where the magic lands)

🔥 OPTIONS 🔥

every single flag, every single default, nothing skipped because we are thorough and that's the vibe:

• --ctg2ctg_file=STRING — filename containing overlaps between contigs. default: "" 💀 (yes bestie, empty string, it just starts empty)
• --read_min_length=INT — minimum rawread length. default: 10000
• --ctg_min_length=INT — minimum contig length. default: 500
• --read2ctg_min_identity=DOUBLE — minimum identity of overlaps between rawreads and contigs. default: 80
• --ctg2ctg_min_identity=DOUBLE — minimum identity of overlaps between contigs. default: 95
• --read2ctg_max_overhang=INT — maximum overhang of overlaps between rawreads and contigs. default: 500
• --ctg2ctg_max_overhang=INT — maximum overhang of overlaps between contigs. default: 100
• --read2ctg_min_aligned_length=INT — minimum aligned length of overlaps between rawreads and contigs. default: 5000
• --ctg2ctg_min_aligned_length=INT — minimum aligned length of overlaps between contigs. default: 2000
• --read2ctg_min_coverage=INT — minimum coverage of links between rawreads and contigs. default: 4
• --min_contig_length=INT — minimum length of bridged contig. default: 500
• --output_directory=STRING — directory for output files. default: "."
• --select_branch="no|best" — selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch. default: "no" 🌈
• --dump — for testing, dump intermediate files. 🙈 (it's literally labelled "for testing", so like, that's what it's for)
• --thread_size=INT — number of threads. default: 4

🦋 THE SEQUEL (a.k.a. the part where it says all of that again) 🦋

ngl the manpage really said "run it back" and repeated the whole thing, and because I keep every detail, here it is in full, exactly as it appears. main character energy twice. 💅✨

Usage: fsa_ctg_bridge [options] rawreads contigs read2ctg bridged_contigs

• rawreads — rawread file 📖
• contigs — contig file 🧵
• read2ctg — file containing overlaps between rawread and contigs 🔗
• bridged_contigs — output file 🎀

and the options, one more time, because consistency is hot:

• --ctg2ctg_file=STRING — filename containing overlaps between contigs. default: ""
• --read_min_length=INT — minimum rawread length. default: 10000
• --ctg_min_length=INT — minimum contig length. default: 500
• --read2ctg_min_identity=DOUBLE — minimum identity of overlaps between rawreads and contigs. default: 80
• --ctg2ctg_min_identity=DOUBLE — minimum identity of overlaps between contigs. default: 95
• --read2ctg_max_overhang=INT — maximum overhang of overlaps between rawreads and contigs. default: 500
• --ctg2ctg_max_overhang=INT — maximum overhang of overlaps between contigs. default: 100
• --read2ctg_min_aligned_length=INT — minimum aligned length of overlaps between rawreads and contigs. default: 5000
• --ctg2ctg_min_aligned_length=INT — minimum aligned length of overlaps between contigs. default: 2000
• --read2ctg_min_coverage=INT — minimum coverage of links between rawreads and contigs. default: 4
• --min_contig_length=INT — minimum length of bridged contig. default: 500
• --output_directory=STRING — directory for output files. default: "."
• --select_branch="no|best" — selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch. default: "no"
• --dump — for testing, dump intermediate files. 🙈
• --thread_size=INT — number of threads. default: 4

ok and that's literally the whole page bestie. go bridge some contigs, you're gonna eat. 🍓💜

mwah 💋 that was fsa_ctg_bridge, filed under Bridge contigs, dated July 2020 — see you in the next manpage, love u, bye!! 🎀🦋✨