Naive question. I do not quite understand in what situations the postprocessing option -g would be useful (use gapped alignments when attempting to rescue pairs). Thoughts?
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If you are trying to rescue the other read considering the to-be-rescued end with indels the gapped method is useful. I find that it overfits by calling falsely indels in many cases. Remember, the rescue relies solely on its pair/mate.Originally posted by Protaeus View Post
I would test both out and see which you are most happy with. Always good to have options (literally).
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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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