Hi, I have over 2 million nucleotide sequence and each sequence is average 30kb in size. I want to run A sequence identity and clustering analysis on that..I tried CD-HIT suite but it falling every time. So is there anything available to run a sequence identity analysis on 2 million sequence? Or any suggestions?
Dear Pratanu,
Sequencing of big data needs a lot of things to be kept in mind before analysis.
https://www.mathworks.com/help/bioinfo/sequence-analysis.html
https://www.mathworks.com/discovery/cluster-analysis.html
Article KClust: Fast and sensitive clustering of large protein seque...
https://academic.oup.com/nar/article/46/14/e83/4990634
https://www.nature.com/articles/s41467-018-04964-5
https://medcraveonline.com/MOJPB/how-to-cluster-protein-sequences-tools-tips-and-commands.html
Dear Pratanu Kayet
These links might be useful, have a look:
1. https://www.mathworks.com/help/stats/kmeans.html
2. https://www.mathworks.com/help/stats/evalclusters.html
3. https://www.mathworks.com/discovery/cluster-analysis.html
4. https://www.mathworks.com/help/bioinfo/sequence-analysis.html
5. https://github.com/torognes/swarm
6. https://github.com/biobakery/humann
7. https://github.com/biobakery/cgfp/blob/master/README.md
Kind Regards
Qamar Ul Islam
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