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Old 12-05-2011, 06:49 AM   #1
Estefania
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Location: Rosario, Argentina

Join Date: Feb 2011
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Default How to get assembly metrics from (AMOS) minimus and minimo assemblies?

Hi everybody!

Recently, I tried the assemblers minimus and minimo from the AMOS v3.1.0 package to assemble a bacteria de novo using 454 Titanium reads.

However, although the assemblies finished ok (no errors reported) I couldn't find out an assembly metrics file like when using Newbler (454NewblerMetrics.txt) or Mira (bacteria_info_assembly.txt).

Does anybody knows how to obtain this data from these assemblers (minimus and minimo)?

Thank you very much in advance.

Regards,

Estefi
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Old 12-17-2011, 06:11 AM   #2
Ole
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Location: Oslo, Norway

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Default

Not all assemblers output as detailed information as Newbler does, but I've been using the assemblathon_stats.pl script (http://assemblathon.org/assemblathon...sembly-metrics), to get the basic info about N50, mean, longest, etc., from my assemblies.
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