MAPSEMBLER2_KISSREADS_GRAPH(1)

💅 MAPSEMBLER2_KISSREADS_GRAPH — the manual page, but make it make sense 💅

okay bestie, so this is the manpage for mapsembler2_kissreads_graph from section 1 of the User Commands manual. it's giving graph-mapping realness and honestly? it ate. let's get into it 🫶

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✨ NAME ✨

mapsembler2_kissreads_graph — maps the provided reads on the graph 🦋

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🌸 SYNOPSIS 🌸

mapsembler2_kissreads_graph input_graph <readsC1.fasta/fastq[.gz]>
[<readsC2.fasta/fastq[.gz]> [<readsC3.fasta/fastq[.gz] ...] -M -t type
[-k value] [-c min_coverage] [-d max_substitutions] [-o name] [-h]

so like. you hand it a graph, you hand it reads, and it does the thing. the reads can be .fasta or .fastq and they can be gzipped (.gz) because we're not savages 💖 and yeah you can stack up as many read files as you want, <readsC2> , <readsC3> , and so on forever, iykyk.

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👑 DESCRIPTION 👑

mapsembler2_kissreads_graph maps the provided reads on the graph. no cap, that's the whole job. 💅

with the option -t coverage it outputs an equivalent graph that removes uncovered edges and then adds:

• for each node: the coverage per sample and per position ✨
• for each edge: the number of mapped reads per sample using this edge 🌈

with the option -t modify it outputs the same simplified graph, going through:

• removing low covered edges and nodes (less that min_coverage) 🧚
• then phasing simple non branching paths ⭐

and if you pass -M, the input is considered as a Mapsembler output — which means it's composed of multiple independent graphes 🦋 (yes, "graphes", that's what it says, we respect the original spelling here, periodt).

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🎀 OPTIONS 🎀

💖 MANDATORY 💖

like you literally cannot skip these, bestie, they're mandatory for a reason 😭

• -t <type> — the type. it's giving "pick one":
  • "c" "coverage" — the coverage vibe 🌸
  • "m" "modify" — the modify vibe 🔥

🦋 OPTIONAL 🦋

these ones are the fun little extras, the accessories to the outfit 💅

• -M — the input is considered as a Mapsembler output 👑
• -o file_name — write obtained graph. default: standard output (so if you say nothing, it just spills out at you, main character energy)
• -k size_seed — will use seeds of length size_seed. default: 25. 🌱
• -c min_coverage — will consider an edge as coherent if coverage (number of reads from all sets using this edge) is at least min_coverage. default: 2 ✨
• -d max_substitutions — will map a read on the graph with at most max_substitutions substitutions. default: 1 🙈

also -h is hanging out in the synopsis up there, being mysterious. the page doesn't describe it further and neither will i — i'm not out here inventing lore, that's not the vibe 💀

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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. thank you Andreas, you absolute icon 🫶

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and that's the whole thing!! mapsembler2_kissreads_graph 2.2.4, October 2018 — mwah, go map some reads, bestie, you got this 💖✨🎀🦋🌸💅