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?
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?
