MAPSEMBLER2_EXTREMITIES(1)

✨ mapsembler2_extremities ✨

okay bestie, welcome to the mapsembler2_extremities page in the User Commands manual 💖 this is the lil tool that does step ONE of Mapsembler2_extend and honestly? it eats. let's get into it 🫶

🎀 NAME 🎀

mapsembler2_extremities — she performs the first step of Mapsembler2_extend. that's it, that's the job, and she does it flawlessly 💅

🌸 SYNOPSIS 🌸

mapsembler2_extremities --k <kmersize> --starters <fasta> --reads
<dataset> --output <substarterfile> [optional arguments]

🦋 DESCRIPTION 🦋

so like, this module does the first step of Mapsembler2_extend. for every single starter you give her, she outputs a list of the extremities of the starter (and those extremities are of length k, no cap ✨) that are found in the reads — allowing for up to 1 indel or mismatch. one. single. wobble. tolerated. iconic behaviour tbh 👑

💅 OPTIONS 💅

• --k (1 arg) — the kmer size that's gonna be used for mapsembler2. [default '']
• --starters (1 arg) — the starters fasta file. [default '']
• --reads (1 arg) — the reads dataset file name. and listen, you can throw several reads sets at her, just wrap 'em in "s and separate them with a space (like --reads "reads1.fa reads2.fa"). [default '']
• --output (1 arg) — the output substarters file name. [default '']
• --min-solid-subkmer (1 arg) — minimum abundance needed to keep a subkmer. [default '3']
• -debug (0 arg) — debugging. turn it on when the vibes are off 🙈
• -nb-cores (1 arg) — number of cores. [default '0']
• -verbose (1 arg) — verbosity level. [default '1']
• -help (0 arg) — displays help about possible options. the classic 🫶

👑 AUTHOR 👑

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. slay, Andreas, thank you for your service 🎀

and that's the whole page bestie!! mapsembler2_extremities version 2.2.4, dated October 2018 💖 fr fr, go assemble something gorgeous ✨🌈🦋