Update clustering method
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4.2 years ago

In my faculty, we use ion torrent. After the trimming and fastq analysis, we perform clustering with usearch based on the identity of the reads length. However, I want to know if there is a new way to perform clustering. I'm sorry if this is a not so interesting question. Thanks

clustering sequencin • 552 views
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What are you clustering? Please add details.

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I assume you are clustering reads to identify sequence duplicates. Take a look at clumpify.sh and its features here: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates. If some of reads are expected to be shorter (i.e contained in others) then you will need to use containment=t option.

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I will see your suggestion @genomex, thanks!

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