Question: Update clustering method
0
gravatar for anasofiamoreira94
9 weeks ago by
anasofiamoreira9470 wrote:

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 • 92 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by anasofiamoreira9470
2

What are you clustering? Please add details.

ADD REPLYlink written 9 weeks ago by ATpoint35k
2

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.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax84k

I will see your suggestion @genomex, thanks!

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by anasofiamoreira9470
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