Does anyone do contig analysis

[dkatzel]

I posted a similar question in the General Forum a few weeks ago but didn't get any responses. Are there any good libraries for programmatic contig analysis (detecting variations, coverage problems, sequence errors , assembly errors etc). I see that BioJava doesn't have any kind of contig object representation and while BioPerl and BioPython frameworks have contig objects, there doesn't appear to be any built-in analysis methods.

[samanta]

What kind of sequences do you have - microbial, eukaryote, vertebrate? I have several custom pipelines, plus can guide you to few programs made by others.

[dkatzel]

I work with all kinds of data. I have found that lots of people have written custom pipelines that string together a wide variety of tools. Each tool only give a partial answer to the question they want to know. Also many of the tools require different input formats and have their own unique output formats so most of the pipeline is actually only doing format conversion and output parsing.

I was hoping there was a "one stop shop" framework or library that would work for all sizes of genomes that would allow the bio-informatician to programmatically do the specific analysis they wanted.