Cleaning second-generation sequencing data - current situation

[xApple]

Hello everyone,

What was first to be a question on seqanswers or biostars, turned into a long post as I was writting it, so I ended up loading it on a blog. But it's not less of topic I would like to see discussed here or else where. I would be grateful if you felt like sharing your thoughts about the pre-processing of reads. Here is the link to my short review:

Cleaning second-generation sequencing data

[yaximik]

Thanks for making this review. I am scouring the net for such set of tools/software myself. I noticed though that you focused on 454 reads, I guess because of your data set, is that correct? I have a mix of Illumina/454 reads, so my only option is using fastq format as input. I would also appreciate to hear opinion/advice on that from more seasoned members.

[xApple]

Yes, that is correct, my data is exclusively 454. But that will probably soon change. It's a pity that this thread did not take up. The last post on cleaning data generated 25 replies.