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--- archive:bioinformatic_tools:mira [2010/05/12 19:20]
mpcusack
+++ archive:bioinformatic_tools:mira [2015/09/04 09:06] (current)
68.180.228.52 ↷ Links adapted because of a move operation
@@ Line 20: / Line 20: @@
   make install
-This added the following binaries to the [[computer_resources:bin|bin]] directory
+This added the following binaries to the [[archive:computer_resources:bin|bin]] directory
 <code>-rwxr-xr-x+  1 mcusack  bme235  3.0M Apr 11 21:18 convert_project
 -rwxr-xr-x+  1 mcusack  bme235   11K Apr 11 21:18 fasta2frag.tcl
@@ Line 33: / Line 33: @@
 </code>
-====Use====
+====Internals===
+Slides from a presentation dated 5/17 by Michael Cusack summarizing how MIRA works {{:bioinformatic_tools:mira_internals.pdf|}}.
 ====Assemblies===
-A list of assemblies using MIRA can be found [[computer_resources:assemblies:mira|here]].
+A list of assemblies using MIRA can be found [[archive:computer_resources:assemblies:mira|here]].
-Currently just one assembly has been performed with MIRA using //Pyrobaculum oguniense// data.
+Currently just two assembies have been performed with MIRA using //Pyrobaculum oguniense// data.
+====Conclusions====
+MIRA appears to be a very good assembler for denovo data. It's strengths are that it can take in many types of data tries to use all data to the fullest while keeping quality of the results high. Based on tests there appears to be occasional problems with chimeric contigs in the results, but this was fixed by specifying more stringent settings.
+Disadvantages are mainly its speed and memory requirements. Assembling Pog took 13 hours, and mira estimates it would need 1.1 TB of memory to assemble the banana slug (using data available May 2010). Documentation is also spotty and often outdated. The thesis referenced on this page is the most complete reference of how MIRA works, but it is several years (and versions) old. Some later documentation mentions that parts of the processing have changed in recent versions, but do not specify what or how.

Banana Slug Genomics

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