Chimeric reads hard clipping
Hello, everyone. I got a question without answer after a long exhaustive liaterature search. I am using multiple displacement amplification (MDA) to amplify my samples, followed by 454 sequencing. MDA is well known for the generation of chimera, and therefore chimeric reads. In my dataset, nearly 30% reads are chimeric, estimated by Bowtie 2 aligner. I wonder whether there are some tools can retrieve the mapped domains of chimeric reads only from SAM output. If yes, I think this may break chimeric reads into single mappable reads.
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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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