FSA_ASSEMBLE(1)

🌸 FSA_ASSEMBLE(1) — the vibe check 🌸

okay so bestie, welcome to FSA_ASSEMBLE(1) from the User Commands section. it's literally giving "construct contigs" energy, no cap. 💅

💖 NAME 💖

fsa_assemble - Constructs contigs from filtered overlaps and corrected reads

that's the whole name, bestie. iconic.

✨ SYNOPSIS ✨

fsa_assemble [options] filterd_overlaps

yes, filterd_overlaps is spelled exactly like that, and we are keeping it exactly like that. facts don't change. 🫶

💜 DESCRIPTION 💜

Bestie, fsa_assemble constructs contigs from filtered overlaps and corrected reads. that's the main character move right there. it takes filtered overlaps and corrected reads and makes contigs. slay. ✨

🎀 OPTIONS 🎀

okay so here's the menu of flags, lowkey iconic:

• --min_length=INT — minimum length of reads default: 0
• --min_identity=DOUBLE — minimum identity of overlaps default: 0
• --min_aligned_length=INT — minimum aligned length of overlaps default: 0
• --min_contig_length=INT — minimum length of contigs default: 500
• --read_file=STRING — read filename default: ""
• --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: ""
• --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"
• --thread_size=INT — number of threads default: 1
• --dump=INT — for testing, dump intermediate files default: 0
• --run_mode=INT — for testing default: 4
• --lfc — deprecated, for testing
• --remove_chimer — deprecated, remove chimer node

and then the manual drops the usage line like it's a surprise:

Usage: fsa_assemble [options] filterd_overlaps

filterd_overlaps — input filename

and then, not me seeing the whole option list again, but here we are, and we're keeping every single crumb:

• --min_length=INT — minimum length of reads default: 0
• --min_identity=DOUBLE — minimum identity of overlaps default: 0
• --min_aligned_length=INT — minimum aligned length of overlaps default: 0
• --min_contig_length=INT — minimum length of contigs default: 500
• --read_file=STRING — read filename default: ""
• --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: ""
• --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"
• --thread_size=INT — number of threads default: 1
• --dump=INT — for testing, dump intermediate files default: 0
• --run_mode=INT — for testing default: 4
• --lfc — deprecated, for testing
• --remove_chimer — deprecated, remove chimer node

deprecated alert: --lfc and --remove_chimer are deprecated, bestie. they're still listed, so we're still listing them. periodt.

okay bestie, that's the whole manual. this one is FSA_ASSEMBLE(1), dated July 2020, and the footer text was Constructs contigs from filtere... 💖✨ no cap.