Swarm v2: highly-scalable and high-resolution amplicon clustering
Abstract
Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.
Keywords
Medicine
Engineering (General). Civil engineering (General)
Information technology
Technology
Science (General)
neurology. diseases of the nervous system
social sciences (general)
special aspects of education
mathematics
electronic computers. computer science
industrial engineering. management engineering
mining engineering. metallurgy
computer software
probabilities. mathematical statistics
Access
Citation
ID:
54004
References
Blockchain Verification
Account:
NFT Contract Address:
0x95644003c57E6F55A65596E3D9Eac6813e3566dA
Article ID:
54004
Unique Identifier:
Network:
Scimatic Chain (ID: 481)
Loading...
Blockchain Readiness Checklist
Authors
Abstract
Journal Name
Year
Title
Creates 1,000,000 NFT tokens for this article
Token Features:
- ERC-1155 Standard NFT
- 1 Million Supply per Article
- Transferable via MetaMask
- Permanent Blockchain Record
Scan with Saymatik Web3.0 Wallet
