MAPSEMBLER_EXTEND(1)

✨ MAPSEMBLER_EXTEND ✨

okay bestie, so mapsembler_extend is a User Command and it is literally the main character of targeted micro assembly. it takes a DNA sequence you care about, throws a pile of reads at it, and extends it. that's the whole vibe. 💅

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🌸 NAME 🌸

mapsembler_extend — extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly.

yes that's it. that's the gig. slay.

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🦋 SYNOPSIS 🦋

mapsembler_extend <extrem_kmers.fasta> <readsC1.fasta> [<readsC2.fasta>
[<readsC3.fasta] ...] [-t extension_type] [-k value] [-c value] [-g
value] [-i index_name] [-o name] [-h]

so like. you give it your <extrem_kmers.fasta> first, then at least one reads file <readsC1.fasta>, and if you have more reads files you just keep stacking them <readsC2.fasta>, <readsC3.fasta>, ... like it's a group chat that keeps adding members. then all the optional flags. periodt.

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💖 DESCRIPTION 💖

Mapsembler 2 extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly.

that's the actual official description and ngl it's kinda the whole thing? targeted. micro. assembly. obsessed. 🧚

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✨ OPTIONS ✨

• -t extension_type. Default: 1

okay so this one decides what kind of sequence you get out the other side, and there are FOUR flavours:

1. a strict sequence: any branching stops the extension. like, branching shows up and it's over, no discussion.
2. a consensus sequence: contiging approach.
3. a strict graph: any branching is conserved in the graph. nothing gets merged, everything stays, iconic honestly.
4. a consensus graph: "small" polymorphism is merged, but "large" structures are represented. lowkey the best of both worlds fr fr.

• -k size_kmers — size of the k-mers used during the extension phase. Default: 31. the accepted range depends on the compilation — like make k=42 for instance. so if you want a different range, that's a compile-time decision, not a runtime one, bestie.
• -c min_coverage — a sequence is covered by at least min_coverage coherent reads. Default: 2.
• -g estimated_genome_size — estimation of the size of the genome whose reads come from.

it's in bp, does not need to be accurate, only controls memory usage. Default: 3 billion. yes THREE BILLION. casual. 💀

• -x node_len — limit max of nodes length. Default: 40.
• -y graph_max_depth — limit max of graph depth. Default: 10000.
• -i index_name — stores the index files in files starting with this prefix name. can be re-used later. Default: "index".

⚠️ IF THE FILE index_name.bloom EXISTS: the index is not re-created. so heads up, if you wanted a fresh index, that file existing means you're getting the old one. no cap.

• -o file_name_prefix — where to write outputs. Default: "res_mapsembler".
• -p search_mod — kind of process, Breadth or Depth. Default: Breadth. pick your fighter 🫶
• -h — prints this message and exit. the classic. the little escape hatch. we love her.

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🎀 AUTHOR 🎀

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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okay that's the whole page, you're fully caught up, go extend something 💜

mapsembler_extend 2.2.4 — October 2018 — that's the version and the date, mwah, bye bestie 🌈⭐