I do some work for a small diagnostics company that has a requirement for small indel detection in 454 data. Those of you familiar with Roche's pipeline will be aware that AVA (Amplicon Variant Analyzer) blissfully ignores indels <3bp. The 454 is also subject to issues with homopolymer runs.
I'd like to try some alternatives to AVA that focus more on indel than SNP discovery (although SNP discovery is still useful).
So far my inexhastive list of possibilities is:
Does anyone have any experience of these packages for indel calling with 454 data? Or any additional suggestions? We have looked at certain commercial packages, but they tend to come up slightly short on features, largely ones of scriptability/automation.