Newbler and Celera have maximum read lengths of ~2048bp I believe. I've got a few libraries of Sanger random shear that have read lengths a little larger than that. I've also got several libs of 454 data, assembled with newbler into contigs, and several libs of Illumina, assembled with velvet and/or CLC into contigs. What's the best option to overlap all these (reasonably large) contigs into a new assembly?
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I always reach for some "standard" overlap assembler like phrap or AMOS-minimus. Although it doesn't always work as well as I'd like / expect. Interested to hear your experiences. Celera might be another option. -
Cap3 can be one possibility too. Velvet also work to long reads with "-long" parameter.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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