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Old 11-24-2012, 03:30 AM   #1
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Location: China

Join Date: Sep 2009
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Default How to assess Phrap assembly result


Currently I was running Phrap for re-assemble of my transcriptome data-set.
The command that I run for Phrap is shown as below:
phrap -minscore 100 -ace assembly.contig.fna

Can I know how to assess the re-assembly done by Phrap whether is good or bad?
Initial assembly contig gives 369,546 seq, total bases 301,280,040, N50 is 2,077;
Phrap re-assembly gives singlets + contigs gives 88,136 + 120,205 = 208,143 seq, total bases 300,282,588, N50 is 2,370;

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