I've heard that trimming is not as efficient as alignment in the pipeline and then building up or down from there.
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Could you elaborate? What do you mean by 'efficient'?Comment
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i think the small rna pipeline will use the adapter sequence to more efficiently trim reads. It's better to run them as 35bp than to trim them and try and map.Comment
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cutadapt and most trimmers I know do use the adapter sequence to trim the reads (they align the adapter sequence to the end of the read). The alternative is to unconditionally remove the last x bases (or colors) of each read. I do not consider that to be adapter removal, it is way too inaccurate.Comment
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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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