RUN_MAPSEMBLER2_PIPELINE(1)

💖 run_mapsembler2_pipeline — the manual page, but make it make sense 💖

okay bestie, welcome to run_mapsembler2_pipeline (man page section 1, User Commands, obviously 💅). it's a whole pipeline for the mapsembler2 tools and i'm gonna walk you through every single flag because that's what we do here. no skips, no "you'll figure it out", we're going all the way through. 🫶

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✨ NAME ✨

run_mapsembler2_pipeline — it pipelines the mapsembler2 tools. that's it, that's the name, that's the vibe. 🎀

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✨ SYNOPSIS ✨

run_mapsembler_and_phaser.sh -s <starter.fasta> -r <reads.faste> -t [1/2/3/4]<options>

that's the whole summoning ritual. -s, -r, -t, and then whatever options your heart desires. 🌸

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✨ DESCRIPTION ✨

so like, run_mapsembler_pipeline.sh is the little script that does the pipelining — it strings together mapsembler2_extremities, mapsembler2_extend and kissread_g. it's giving backstage crew energy. the main characters get the credit but nothing runs without them. 👑

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✨ OPTIONS ✨

these three are the ones you actually have to pass, bestie. no skipping. 🚨

• -s — the file containing your starters, in fasta format. your starting points, your little seedlings. 🌱
• -r — a list of reads separated by space, surrounded by the " character. and listen — the reads can be in fasta or fastq format, gzipped or not, she's flexible like that 💁‍♀️. Example: -r "data_sample/reads_sequence1.fasta data_sample/reads_sequence2.fasta.gz".
• -t — the kind of assembly you want. pick your fighter:
  • 1 = unitig (fasta)
  • 2 = contig (fasta)
  • 3 = unitig (graph)
  • 4 = contig(graph)

not me pointing out that 4 is written as 4=contig(graph) with no space. i'm keeping it exactly as it is because we do not editorialize the facts. periodt. 💅

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✨ OPTIONAL ✨

these are the seasoning ✨. all optional, all useful, all here in full because i would never gatekeep. 🌈

• -p prefix — every output file will start with this prefix. Example: -p my_prefix. it's giving name tags at a party 🎀
• -k value — sets the length of the kmers that get used. it must fit the compiled value (respect the build, she has limits 😭). Default=31. Example: -k 31
• -c value — sets the minimal coverage. Default=5. Example: -c 5
• -d value — sets the number of authorized substitutions used while mapping reads on found SNPs. Default=1. Example: -d 1
• -g value — estimated genome size. it's only used to control memory usage, nothing else. e.g. 3 billion (3000000000) uses 4Gb of RAM. Default=10 million. Example: -d 10000000
• -f value — sets the process of search in the graph (1=Breadth and 2=Depth). Default=1. Example: -f 1
• -x value — sets the maximal nodes length. Default=40. Example: -x 40
• -y value — sets the maximal graph depth. Default=10000. Example: -y 10000
• -h — prints this message and exits. the classic. the icon. the "help me help you" flag. 🫶

okay so about -g: the example literally says -d 10000000 even though we're talking about -g. i am not fixing it, i am not guessing, i am simply reporting the lore as it was written. iykyk 💀

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✨ SEE ALSO ✨

any further question? bestie, read the readme file 📖 or contact us: pierre.peterlongo@inria.fr. they will answer, they're nice like that. 💜

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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. slay, Andreas. 👑✨

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and that's the whole page, fr fr. this was run_mapsembler2_pipeline 2.2.4, dated October 2018. take care of her, she's an icon. 🦋💖🎀

mwah, bye bestie 💅