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I've just finished my first shot at assembling a metagenome sample derived from a marine environment using Velvet, VelvetOptimizer and Metavelvet. Running the assembly with the recommendations from VelvetOptimizer (kmer size of 31), I was getting very short contigs ~100-400 bp. Increasing the kmer size beyond this to 37 resulted in longer contigs 100-3K. When I started analyzing the coverage and reads for several contigs, I noticed that some short contigs i.e. 90bp had about 10K reads and a coverage of 20X for example. Some of the longer contigs 1K or 2K had less reads (200) and lower coverage. My question is if there are certain steps I can take now to filter out contigs that might not be useful in the annotation step for example, or that could be chimeric? I'm not sure how to further proceed. Before I try using a different assembler I'd like to understand how these results could be further analyzed before proceeding to the annotation step.
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