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Ish: Taxonomic and metabolic diversity of microbial communities in a thermal water stream in Uzbekistan and proposal of two new classes of uncultivated bacteria, Desulfocorpusculia class. nov. and Tepidihabitantia class. nov., named following the rules of SeqCode

  1. ModelFinder: fast model selection for accurate phylogenetic estimates

    Subha Kalyaanamoorthy, Bùi Quang Minh, Thomas K. F. Wong +2

    Maqola201724 iqtibos
    ABI

  2. Trimmomatic: a flexible trimmer for Illumina sequence data

    Anthony Bolger, Marc Lohse, Björn Usadel

    Maqola201423 iqtibos
    ABI

  3. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

    Bùi Quang Minh, Heiko A. Schmidt, Olga Chernomor +4

    Maqola202023 iqtibos
    ABI

  4. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

    Anton Bankevich, Sergey Nurk, Dmitry Antipov +13

    Maqola201218 iqtibos
    ABI

  5. DADA2: High-resolution sample inference from Illumina amplicon data

    Benjamin J. Callahan, Paul J. McMurdie, Michael Rosen +3

    Maqola201615 iqtibos
    ABI

  6. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

    Stephen F. Altschul

    Sharh maqola199714 iqtibos
    ABI

  7. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

    Christian Quast, Elmar Pruesse, Pelin Yilmaz +5

    Maqola201212 iqtibos
    ABI

  8. Cutadapt removes adapter sequences from high-throughput sequencing reads

    Marcel Martin

    Maqola201111 iqtibos
    ABI

  9. Ultrafast Approximation for Phylogenetic Bootstrap

    Bùi Quang Minh, Minh Anh Nguyen, A. von Haeseler

    Maqola20139 iqtibos
    ABI

  10. GTDB-Tk v2: memory friendly classification with the genome taxonomy database

    Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz +1

    Maqola20225 iqtibos
    ABI

  11. Salmon provides fast and bias-aware quantification of transcript expression

    Rob Patro, Geet Duggal, Michael I. Love +2

    Maqola20175 iqtibos
    ABI

  12. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

    Ross Overbeek, Robert Olson, Gordon D. Pusch +11

    Maqola20134 iqtibos
    ABI

  13. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

    Donovan H. Parks, Michael Imelfort, Connor T. Skennerton +2

    Maqola20154 iqtibos
    ABI

  14. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

    Dongwan Kang, Feng Li, Edward Kirton +4

    Maqola20194 iqtibos
    ABI

  15. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

    Dongwook Kim, Sein Park, Jongsik Chun

    Maqola20214 iqtibos
    ABI

  16. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    Thomas Brettin, James J. Davis, Terry Disz +13

    Maqola20153 iqtibos
    ABI

  17. NCBI prokaryotic genome annotation pipeline

    Tatiana Tatusova, Michael DiCuccio, Azat Badretdin +7

    Maqola20163 iqtibos
    ABI

  18. Bergey's Manual of Systematics of Archaea and Bacteria

    Kitob20153 iqtibos
    ABI

  19. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

    Donovan H. Parks, Maria Chuvochina, Christian Rinke +3

    Maqola20213 iqtibos
    ABI

  20. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

    Yu‐Wei Wu, Blake A. Simmons, Steven W. Singer

    Maqola20153 iqtibos
    ABI

  21. Binning metagenomic contigs by coverage and composition

    Johannes Alneberg, Brynjar Smári Bjarnason, Ino de Bruijn +7

    Maqola20143 iqtibos
    ABI

  22. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

    Robert M. Bowers, Nikos C. Kyrpides, Ramūnas Stepanauskas +51

    Maqola20173 iqtibos
    ABI

  23. Analysis of 16S rRNA Primer Systems for Profiling of Thermophilic Microbial Communities

    Alexander Y. Merkel, I. Yu. Tarnovetskii, Olga A. Podosokorskaya +1

    Maqola20193 iqtibos
    ABI

  24. A complete domain-to-species taxonomy for Bacteria and Archaea

    Donovan H. Parks, Maria Chuvochina, Pierre-Alain Chaumeil +3

    Maqola20203 iqtibos
    ABI

  25. IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

    Ilias Lagkouvardos, Divya Joseph, Martin Kapfhammer +4

    Maqola20162 iqtibos
    ABI