227 related articles for article (PubMed ID: 35902092)
1. Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake.
Thompson LR; Anderson SR; Den Uyl PA; Patin NV; Lim SJ; Sanderson G; Goodwin KD
Gigascience; 2022 Jul; 11():. PubMed ID: 35902092
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. 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]
4. Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments.
Ansorge R; Birolo G; James SA; Telatin A
Int J Mol Sci; 2021 May; 22(10):. PubMed ID: 34069990
[TBL] [Abstract][Full Text] [Related]
5. ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications.
Herrick N; Walsh S
BMC Bioinformatics; 2023 Nov; 24(1):424. PubMed ID: 37940870
[TBL] [Abstract][Full Text] [Related]
6. StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies.
Bacci G; Bazzicalupo M; Benedetti A; Mengoni A
Mol Ecol Resour; 2014 Mar; 14(2):426-34. PubMed ID: 24128146
[TBL] [Abstract][Full Text] [Related]
7. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.
Bokulich NA; Kaehler BD; Rideout JR; Dillon M; Bolyen E; Knight R; Huttley GA; Gregory Caporaso J
Microbiome; 2018 May; 6(1):90. PubMed ID: 29773078
[TBL] [Abstract][Full Text] [Related]
8. RESCRIPt: Reproducible sequence taxonomy reference database management.
Robeson MS; O'Rourke DR; Kaehler BD; Ziemski M; Dillon MR; Foster JT; Bokulich NA
PLoS Comput Biol; 2021 Nov; 17(11):e1009581. PubMed ID: 34748542
[TBL] [Abstract][Full Text] [Related]
9. CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis.
Hupfauf S; Etemadi M; Fernández-Delgado Juárez M; Gómez-Brandón M; Insam H; Podmirseg SM
PLoS One; 2020; 15(12):e0243241. PubMed ID: 33264369
[TBL] [Abstract][Full Text] [Related]
10. ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis.
Rivers AR; Weber KC; Gardner TG; Liu S; Armstrong SD
F1000Res; 2018; 7():1418. PubMed ID: 30416717
[TBL] [Abstract][Full Text] [Related]
11. Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package.
Lawley B; Tannock GW
Methods Mol Biol; 2017; 1537():153-163. PubMed ID: 27924593
[TBL] [Abstract][Full Text] [Related]
12. crabs-A software program to generate curated reference databases for metabarcoding sequencing data.
Jeunen GJ; Dowle E; Edgecombe J; von Ammon U; Gemmell NJ; Cross H
Mol Ecol Resour; 2023 Apr; 23(3):725-738. PubMed ID: 36437603
[TBL] [Abstract][Full Text] [Related]
13. SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data.
Dufresne Y; Lejzerowicz F; Perret-Gentil LA; Pawlowski J; Cordier T
BMC Bioinformatics; 2019 Feb; 20(1):88. PubMed ID: 30782112
[TBL] [Abstract][Full Text] [Related]
14. PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes.
Zafeiropoulos H; Viet HQ; Vasileiadou K; Potirakis A; Arvanitidis C; Topalis P; Pavloudi C; Pafilis E
Gigascience; 2020 Mar; 9(3):. PubMed ID: 32161947
[TBL] [Abstract][Full Text] [Related]
15. ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently.
Tian R; Imanian B
BMC Bioinformatics; 2022 Jan; 23(1):27. PubMed ID: 34991446
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. Automation of QIIME2 Metagenomic Analysis Platform.
Fung C; Rusling M; Lampeter T; Love C; Karim A; Bongiorno C; Yuan LL
Curr Protoc; 2021 Sep; 1(9):e254. PubMed ID: 34554657
[TBL] [Abstract][Full Text] [Related]
18. CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.
Pandey RV; Nolte V; Schlötterer C
BMC Res Notes; 2010 Jan; 3():3. PubMed ID: 20180949
[TBL] [Abstract][Full Text] [Related]
19. ARMOR: An
Orjuela S; Huang R; Hembach KM; Robinson MD; Soneson C
G3 (Bethesda); 2019 Jul; 9(7):2089-2096. PubMed ID: 31088905
[TBL] [Abstract][Full Text] [Related]
20. AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology.
Min D; Doxey AC; Neufeld JD
Gigascience; 2021 Feb; 10(2):. PubMed ID: 33533410
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
