214 related articles for article (PubMed ID: 31894129)
1. A critical analysis of state-of-the-art metagenomics OTU clustering algorithms.
Bhat AH; Prabhu P; Balakrishnan K
J Biosci; 2019 Dec; 44(6):. PubMed ID: 31894129
[TBL] [Abstract][Full Text] [Related]
2. hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Units Based on Homopolymer Compaction.
Park S; Choi HS; Lee B; Chun J; Won JH; Yoon S
IEEE/ACM Trans Comput Biol Bioinform; 2018; 15(2):441-451. PubMed ID: 26930691
[TBL] [Abstract][Full Text] [Related]
3. OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes.
Yadav D; Dutta A; Mande SS
DNA Res; 2019 Apr; 26(2):147-156. PubMed ID: 30624596
[TBL] [Abstract][Full Text] [Related]
4. Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering.
Franzén O; Hu J; Bao X; Itzkowitz SH; Peter I; Bashir A
Microbiome; 2015 Oct; 3():43. PubMed ID: 26434730
[TBL] [Abstract][Full Text] [Related]
5. A De Novo Robust Clustering Approach for Amplicon-Based Sequence Data.
Bazin A; Debroas D; Mephu Nguifo E
J Comput Biol; 2019 Jun; 26(6):618-624. PubMed ID: 30517025
[No Abstract] [Full Text] [Related]
6. DBH: A de Bruijn graph-based heuristic method for clustering large-scale 16S rRNA sequences into OTUs.
Wei ZG; Zhang SW
J Theor Biol; 2017 Jul; 425():80-87. PubMed ID: 28454900
[TBL] [Abstract][Full Text] [Related]
7. LotuS: an efficient and user-friendly OTU processing pipeline.
Hildebrand F; Tadeo R; Voigt AY; Bork P; Raes J
Microbiome; 2014 Sep; 2(1):30. PubMed ID: 27367037
[TBL] [Abstract][Full Text] [Related]
8. CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.
Oh J; Choi CH; Park MK; Kim BK; Hwang K; Lee SH; Hong SG; Nasir A; Cho WS; Kim KM
PLoS One; 2016; 11(3):e0151064. PubMed ID: 26954507
[TBL] [Abstract][Full Text] [Related]
9. HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies.
Zheng Q; Bartow-McKenney C; Meisel JS; Grice EA
Genome Biol; 2018 Jun; 19(1):82. PubMed ID: 29950165
[TBL] [Abstract][Full Text] [Related]
10. DNACLUST: accurate and efficient clustering of phylogenetic marker genes.
Ghodsi M; Liu B; Pop M
BMC Bioinformatics; 2011 Jun; 12():271. PubMed ID: 21718538
[TBL] [Abstract][Full Text] [Related]
11. Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting.
Nguyen TD; Schmidt B; Zheng Z; Kwoh CK
IEEE/ACM Trans Comput Biol Bioinform; 2015; 12(5):1060-73. PubMed ID: 26451819
[TBL] [Abstract][Full Text] [Related]
12. MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence.
Chen W; Cheng Y; Zhang C; Zhang S; Zhao H
J Microbiol Methods; 2013 Sep; 94(3):347-55. PubMed ID: 23899776
[TBL] [Abstract][Full Text] [Related]
13. DACE: a scalable DP-means algorithm for clustering extremely large sequence data.
Jiang L; Dong Y; Chen N; Chen T
Bioinformatics; 2017 Mar; 33(6):834-842. PubMed ID: 28025198
[TBL] [Abstract][Full Text] [Related]
14. CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities.
Kondratenko Y; Korobeynikov A; Lapidus A
BMC Bioinformatics; 2020 Jul; 21(Suppl 12):303. PubMed ID: 32703166
[TBL] [Abstract][Full Text] [Related]
15. Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences.
Narayan NR; Weinmaier T; Laserna-Mendieta EJ; Claesson MJ; Shanahan F; Dabbagh K; Iwai S; DeSantis TZ
BMC Genomics; 2020 Jan; 21(1):56. PubMed ID: 31952477
[TBL] [Abstract][Full Text] [Related]
16. From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data.
Mysara M; Njima M; Leys N; Raes J; Monsieurs P
Gigascience; 2017 Feb; 6(2):1-10. PubMed ID: 28369460
[TBL] [Abstract][Full Text] [Related]
17. DySC: software for greedy clustering of 16S rRNA reads.
Zheng Z; Kramer S; Schmidt B
Bioinformatics; 2012 Aug; 28(16):2182-3. PubMed ID: 22730435
[TBL] [Abstract][Full Text] [Related]
18. Metagenome sequence clustering with hash-based canopies.
Rahman MA; LaPierre N; Rangwala H; Barbara D
J Bioinform Comput Biol; 2017 Dec; 15(6):1740006. PubMed ID: 29113561
[TBL] [Abstract][Full Text] [Related]
19. Phylogeny-based classification of microbial communities.
Tanaseichuk O; Borneman J; Jiang T
Bioinformatics; 2014 Feb; 30(4):449-56. PubMed ID: 24369151
[TBL] [Abstract][Full Text] [Related]
20. Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data.
Koskinen K; Auvinen P; Björkroth KJ; Hultman J
J Comput Biol; 2015 Aug; 22(8):743-51. PubMed ID: 25525895
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]