278 related articles for article (PubMed ID: 32703166)
1. 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]
2. Correction to: 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 Aug; 21(1):362. PubMed ID: 32814545
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags.
Chen X; Johnson S; Jeraldo P; Wang J; Chia N; Kocher JA; Chen J
Gigascience; 2018 Mar; 7(3):1-7. PubMed ID: 29267858
[TBL] [Abstract][Full Text] [Related]
5. Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities.
Dacey DP; Chain FJJ
BMC Bioinformatics; 2021 Oct; 22(1):493. PubMed ID: 34641782
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. 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]
8. Joining Illumina paired-end reads for classifying phylogenetic marker sequences.
Liu T; Chen CY; Chen-Deng A; Chen YL; Wang JY; Hou YI; Lin MC
BMC Bioinformatics; 2020 Mar; 21(1):105. PubMed ID: 32171248
[TBL] [Abstract][Full Text] [Related]
9. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome.
Allali I; Arnold JW; Roach J; Cadenas MB; Butz N; Hassan HM; Koci M; Ballou A; Mendoza M; Ali R; Azcarate-Peril MA
BMC Microbiol; 2017 Sep; 17(1):194. PubMed ID: 28903732
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing.
Parikh HI; Koparde VN; Bradley SP; Buck GA; Sheth NU
BMC Bioinformatics; 2016 Dec; 17(1):491. PubMed ID: 27905885
[TBL] [Abstract][Full Text] [Related]
12. An independent evaluation in a CRC patient cohort of microbiome 16S rRNA sequence analysis methods: OTU clustering, DADA2, and Deblur.
Liu G; Li T; Zhu X; Zhang X; Wang J
Front Microbiol; 2023; 14():1178744. PubMed ID: 37560524
[TBL] [Abstract][Full Text] [Related]
13. 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]
14. Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches.
Nearing JT; Douglas GM; Comeau AM; Langille MGI
PeerJ; 2018; 6():e5364. PubMed ID: 30123705
[TBL] [Abstract][Full Text] [Related]
15. Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads.
Welzel M; Lange A; Heider D; Schwarz M; Freisleben B; Jensen M; Boenigk J; Beisser D
BMC Bioinformatics; 2020 Nov; 21(1):526. PubMed ID: 33198651
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.
Weißbecker C; Schnabel B; Heintz-Buschart A
Gigascience; 2020 Nov; 9(12):. PubMed ID: 33252655
[TBL] [Abstract][Full Text] [Related]
18. Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers.
Myer PR; Kim M; Freetly HC; Smith TPL
J Microbiol Methods; 2016 Aug; 127():132-140. PubMed ID: 27282101
[TBL] [Abstract][Full Text] [Related]
19. UPARSE: highly accurate OTU sequences from microbial amplicon reads.
Edgar RC
Nat Methods; 2013 Oct; 10(10):996-8. PubMed ID: 23955772
[TBL] [Abstract][Full Text] [Related]
20. Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.
Lima J; Manning T; Rutherford KM; Baima ET; Dewhurst RJ; Walsh P; Roehe R
J Microbiol Methods; 2021 Jul; 186():106235. PubMed ID: 33974954
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]