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In an attempt to increase the quality of our metagenomic assembly and ensure we capture low abundance species we are co assembling ~20 samples. However after the assembly we need to perform some analysis based on the samples, thus I need to map contigs back to a sample where reads from that sample map to that contig.

I play to just use BWA mem and use coverage as my metric for deciding if a contig should be placed into a sample assembly. However I am unsure at what coverage value I should do this.

Any help would be appreciated

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