mira(1)

💖 mira(1) — the genome & EST sequence assembly system 💖

okay bestie, welcome to mira, from the General Commands Manual section, and honestly? she's a whole legend. let's get into it 🧚

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✨ NAME ✨

mira — The Genome and EST Sequence Assembly System

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🌸 DESCRIPTION 🌸

so. the mira genome and RNA assembler is a specialised assembler for sequencing projects that get classified as 'hard' — and why are they hard? because of a high number of similar repeats. yeah. the messy ones. the ones that make other assemblers cry 😭

and she's not a one-trick pony either, she's routinely out here doing tasks like:

• mutation detection in different cell types
• similarity analysis of transcripts between organisms
• pristine assembly of sequences from various sources, for oligo design in clinical microarray experiments

and like, the whole purpose of the mira executable? to assemble sequencing data. that's the job. that's the vibe. periodt. 💅

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⭐ SYNOPSIS ⭐

mira [OPTION] manifest_file [manifest_file] ...

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💅 OPTIONS 💅

okay here's the menu, no skips, all of them:

• -c / --cwd=directory — change the working directory. like, move the whole operation somewhere else 📁
• -h / --help — print a short help message and dip out. exit, gone, bye 👋
• -m / --mcheck — only check the manifest file, then exit. nothing else. just the vibe check on the manifest 🎀
• -M / --mdcheck — only check the manifest file and whether the data files are actually there, then exit. stricter vibe check, still exits 🔍
• -r / --resume — resume an interrupted assembly. yes bestie, you can pick it back up where it stopped, we don't do starting over in this house 🫶
• -t / --thread — force the number of threads (this overrides the equivalent -GE:not manifest entry, so she wins, no cap) 🧵
• -v / --version — print the version and exit ✨

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🦋 SEE ALSO 🦋

• miraconvert(1)
• mirabait(1)

there's also way more extensive documentation in the MIRA manual, available online at:

http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

on Debian you can just install it with the mira-doc package, and then it lives at /usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. on other systems, maybe peek in /usr/local/share/mira/doc, or just run "locate DefinitiveGuideToMIRA" to find it locally. iykyk 🔎

you can also subscribe to one of the MIRA mailing lists at:

http://www.chevreux.org/mira_mailinglists.html

and after you subscribe (yes, after), mail your general questions to the MIRA talk mailing list:

mira_talk@freelists.org

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💀 BUGS 💀

found a bug? want a feature? please use the ticketing system, don't just scream into the void:

http://sourceforge.net/projects/mira-assembler/

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👑 AUTHOR 👑

the author of the mira code is Bastien Chevreux <bach@chevreux.org>

this manual page was written by Andreas Tille <tille@debian.org> and Bastien Chevreux <bach@chevreux.org> — but it can be freely used for any other distribution. share the love, it's giving generous 💖

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and that's the whole page, bestie!! this one came out of the User Commands corner, dated May 2016, and yeah it's literally mira(1) 🌈 go assemble something iconic 🎀💜