LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

[1] Bahram M(2018)Structure and function of the global topsoil microbiome Nature. 560 233-237

[2] Hildebrand F(2021)Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals Microbiome 9 75-43

[3] Forslund SK(2015)Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi MycoKeys 10 1-504

[4] Anderson JL(2011)Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons Genome Res 21 494-D493

[5] Soudzilovskaia NA(2009)rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea Nucleic Acids Res 37 D489-583

[6] Bodegom PM(2011)Removing noise from pyrosequenced amplicons BMC Bioinformatics 12 38-7541

[7] Bedarf JR(2016)DADA2: high-resolution sample inference from Illumina amplicon data Nat Methods 13 581-857

[8] Beraza N(2009)Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities Appl Environ Microbiol 75 7537-e240

[9] Khazneh H(2019)Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Nat Biotechnol 37 852-1943

[10] Özkurt E(2017)PipeCraft: flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data Mol Ecol Resour 17 e234-2643

[1] Bahram M(2018)Structure and function of the global topsoil microbiome Nature. 560 233-237

[2] Hildebrand F(2021)Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals Microbiome 9 75-43

[3] Forslund SK(2015)Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi MycoKeys 10 1-504

[4] Anderson JL(2011)Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons Genome Res 21 494-D493

[5] Soudzilovskaia NA(2009)rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea Nucleic Acids Res 37 D489-583

[6] Bodegom PM(2011)Removing noise from pyrosequenced amplicons BMC Bioinformatics 12 38-7541

[7] Bedarf JR(2016)DADA2: high-resolution sample inference from Illumina amplicon data Nat Methods 13 581-857

[8] Beraza N(2009)Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities Appl Environ Microbiol 75 7537-e240

[9] Khazneh H(2019)Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Nat Biotechnol 37 852-1943

[10] Özkurt E(2017)PipeCraft: flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data Mol Ecol Resour 17 e234-2643