WinnerTakeAlmostAll: A parsimony approach integrating multi-targets improves marker gene profiling

Amplicon sequencing need to go from using single region to multiple region, one for higher resolution, one for technical replicates. WinnerTakeAlmostAll is an algorithm to calculate a minimum set of references based on the reference-query graph. We showed that this algorithm is superior in resolving species, as well as average out the run effect using technical replicates.

[1]  Carreño Carreño,et al.  Evaluación de la diversidad taxonómica y funcional de la comunidad microbiana relacionada con el ciclo del nitrógeno en suelos de cultivo de arroz con diferentes manejos del tamo , 2020 .

[2]  Daryl M. Gohl,et al.  Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes , 2018 .

[3]  J. Fuhrman,et al.  Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run , 2018, mSystems.

[4]  L. Tedersoo,et al.  PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives. , 2018, The New phytologist.

[5]  Aaron E Darling,et al.  A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq , 2016, PeerJ.

[6]  Dan Knights,et al.  Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies , 2016, Nature Biotechnology.

[7]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[8]  Stephen J. Salipante,et al.  Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling , 2014, Applied and Environmental Microbiology.

[9]  Kessy Abarenkov,et al.  Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide , 2013, The New phytologist.

[10]  Sven Rahmann,et al.  Snakemake--a scalable bioinformatics workflow engine. , 2012, Bioinformatics.

[11]  Yuzhen Ye,et al.  A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes , 2009, PLoS Comput. Biol..

[12]  Aric Hagberg,et al.  Exploring Network Structure, Dynamics, and Function using NetworkX , 2008, Proceedings of the Python in Science Conference.