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Old 01-07-2013, 04:09 AM   #1
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Default Structural variation using paired-end reads

I have resequenced a bacterial genome using paired-end SOLiD reads (75+35 bp).

Which software is recommended to detect large insertions / deletions (and may be other structural variations) which makes use of the paired-end data?

I tried using LifeScope's LargeIndel detection tool, but apparently it's not very useful for prokaryotic genomes.

Along the same lines: which software would you use if you had Illumina data? Does Illumina have a standard software package to solve such a task?
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indel, paired end reads, structural variation

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