A novice’s guide to analyzing NGS-derived organelle and metagenome data
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Debashish Bhattacharya | Mina Rho | Mina Rho | L. Graf | D. Bhattacharya | H. Yoon | Hae Jung Song | H. Qiu | Hwan Su Yoon | Huan Qiu | JunMo Lee | JunMo Lee | Louis Graf
[1] P. Martone,et al. Evolution of Red Algal Plastid Genomes: Ancient Architectures, Introns, Horizontal Gene Transfer, and Taxonomic Utility of Plastid Markers , 2013, PloS one.
[2] George M. Weinstock,et al. Genomic approaches to studying the human microbiota , 2012, Nature.
[3] Donald Sharon,et al. A single-molecule long-read survey of the human transcriptome , 2013, Nature Biotechnology.
[4] I-Min A. Chen,et al. IMG/M: the integrated metagenome data management and comparative analysis system , 2011, Nucleic Acids Res..
[5] M. Ronaghi,et al. Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.
[6] S. Mocali,et al. Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. , 2010, Research in microbiology.
[7] Vincent J. Magrini,et al. Extending assembly of short DNA sequences to handle error , 2007, Bioinform..
[8] Donald Sharon,et al. Strain Kaplan of Pseudorabies Virus Genome Sequenced by PacBio Single-Molecule Real-Time Sequencing Technology , 2014, Genome Announcements.
[9] S. Pääbo,et al. Mitochondrial genome variation and the origin of modern humans , 2000, Nature.
[10] J. Gilbert,et al. Metagenomics - a guide from sampling to data analysis , 2012, Microbial Informatics and Experimentation.
[11] S. Johnston,et al. ORF-FINDER: a vector for high-throughput gene identification. , 2002, Gene.
[12] Michael Maibaum,et al. Survey of current protein family databases and their application in comparative, structural and functional genomics. , 2005, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.
[13] María Martín,et al. UniProt: A hub for protein information , 2015 .
[14] The Uniprot Consortium,et al. UniProt: a hub for protein information , 2014, Nucleic Acids Res..
[15] J. Rothberg,et al. The development and impact of 454 sequencing , 2008, Nature Biotechnology.
[16] C. Jubin,et al. Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids , 2009, BMC Evolutionary Biology.
[17] Yasubumi Sakakibara,et al. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads , 2012, Nucleic acids research.
[18] S. Salzberg,et al. Alignment of whole genomes. , 1999, Nucleic acids research.
[19] Simon Swindell,et al. Sequence Data Analysis Guidebook , 1996 .
[20] F. Scholz,et al. Comparative Analysis of Different DNA Extraction Protocols: A Fast, Universal Maxi-Preparation of High Quality Plant DNA for Genetic Evaluation and Phylogenetic Studies , 1998, Plant Molecular Biology Reporter.
[21] H. Yoon,et al. Unique repeat and plasmid sequences in the mitochondrial genome of Gracilaria chilensis (Gracilariales, Rhodophyta) , 2015 .
[22] Chao Xie,et al. A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA , 2013, Bioinform..
[23] Dean Laslett,et al. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.
[24] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[25] Siu-Ming Yiu,et al. Meta-IDBA: a de Novo assembler for metagenomic data , 2011, Bioinform..
[26] S. Y. Kim,et al. Complete mitochondrial genome of the marine red alga Grateloupia angusta (Halymeniales) , 2014, Mitochondrial DNA.
[27] Lucian Ilie,et al. SHRiMP2: Sensitive yet Practical Short Read Mapping , 2011, Bioinform..
[28] T. Plasterer,et al. SEQMAN. Contig assembly. , 1997, Methods in molecular biology.
[29] Cecil M. Lewis,et al. Ancient human microbiomes. , 2015, Journal of human evolution.
[30] Thomas Wetter,et al. Genome Sequence Assembly Using Trace Signals and Additional Sequence Information , 1999, German Conference on Bioinformatics.
[31] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[32] Kenneth H. Wolfe,et al. GenomeVx: simple web-based creation of editable circular chromosome maps , 2008, Bioinform..
[33] Mark J. P. Chaisson,et al. Reconstructing complex regions of genomes using long-read sequencing technology , 2014, Genome research.
[34] Konrad H. Paszkiewicz,et al. De novo assembly of short sequence reads , 2010, Briefings Bioinform..
[35] Alla Lapidus,et al. A Bioinformatician's Guide to Metagenomics , 2008, Microbiology and Molecular Biology Reviews.
[36] R Higuchi,et al. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. , 2013, BioTechniques.
[37] Xiaojun Guan,et al. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences , 2012, BMC Genomics.
[38] Ralph Bock,et al. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes , 2007, Current Genetics.
[39] Pelin Yilmaz,et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..
[40] F. Raymond,et al. which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Ray Meta: scalable de novo metagenome assembly and profiling , 2012 .
[41] François Laviolette,et al. Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies , 2010, J. Comput. Biol..
[42] Luis Pedro Coelho,et al. Structure and function of the global ocean microbiome , 2015, Science.
[43] F. Blattner,et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.
[44] A. von Haeseler,et al. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.
[45] Kunihiko Sadakane,et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..
[46] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[47] Katherine H. Huang,et al. Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.
[48] Peter F. Hallin,et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.
[49] Tibor Vellai,et al. A New Aspect to the Origin and Evolution of Eukaryotes , 1998, Journal of Molecular Evolution.
[50] Riccardo Velasco,et al. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome , 2013, BMC Genomics.
[51] R. Vaillancourt,et al. Maternal inheritance of the chloroplast genome in Eucalyptus globulus and interspecific hybrids. , 2001, Genome.
[52] 中尾 光輝,et al. KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース) , 2000 .
[53] M. Ludwig,et al. Transcription Profiling of the Model Cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) Sequencing of cDNA , 2011, Front. Microbio..
[54] P. Bork,et al. A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.
[55] J. Handelsman,et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. , 1998, Chemistry & biology.
[56] A. Weber,et al. Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea , 2013, Current Biology.
[57] Mark J. P. Chaisson,et al. Short read fragment assembly of bacterial genomes. , 2008, Genome research.
[58] B. Lang,et al. Mitochondrial introns: a critical view. , 2007, Trends in genetics : TIG.
[59] Ying Huang,et al. Bioinformatics Applications Note Identification of Ribosomal Rna Genes in Metagenomic Fragments , 2022 .
[60] S. Eddy,et al. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.
[61] Robert C. Edgar,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[62] Caspar Zialor. DNA sequencing with chain terminating inhibitors , 2014 .
[63] Martin Goodson,et al. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. , 2011, Genome research.
[64] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[65] Alexandros Stamatakis,et al. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..
[66] J. Badge. DNA sequencing. , 1998, Methods in molecular biology.
[67] Robert K. Jansen,et al. Automatic annotation of organellar genomes with DOGMA , 2004, Bioinform..
[68] Siu-Ming Yiu,et al. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..
[69] Y. Hahn,et al. Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food , 2011, Applied and Environmental Microbiology.
[70] P. Chain,et al. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. , 2012, Current opinion in biotechnology.
[71] Steven J. M. Jones,et al. Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .
[72] P. Stadler,et al. MITOS: improved de novo metazoan mitochondrial genome annotation. , 2013, Molecular phylogenetics and evolution.
[73] M. Salimans,et al. Rapid and simple method for purification of nucleic acids , 1990, Journal of clinical microbiology.
[74] David Hernández,et al. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.
[75] P. Green,et al. Consed: a graphical tool for sequence finishing. , 1998, Genome research.
[76] J. Humbert,et al. Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget--France). , 2009, Environmental microbiology.
[77] S. Y. Kim,et al. Highly Conserved Mitochondrial Genomes among Multicellular Red Algae of the Florideophyceae , 2015, Genome biology and evolution.
[78] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[79] Yongchao Liu,et al. Parallelized short read assembly of large genomes using de Bruijn graphs , 2011, BMC Bioinformatics.
[80] N. Brisson,et al. Recombination and the maintenance of plant organelle genome stability. , 2010, The New phytologist.
[81] Andreas Wilke,et al. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG , 2011, BMC Bioinformatics.
[82] Robert Olson,et al. Accessing the SEED Genome Databases via Web Services API: Tools for Programmers , 2010, BMC Bioinformatics.
[83] C. Gaillard,et al. Ethanol precipitation of DNA with linear polyacrylamide as carrier. , 1990, Nucleic acids research.
[84] B. Gravendeel,et al. The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.
[85] W. Martin,et al. The hydrogen hypothesis for the first eukaryote , 1998, Nature.
[86] Yongan Zhao,et al. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data , 2011, Bioinform..
[87] Sean R. Eddy,et al. Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..
[88] E. Yang,et al. Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes , 2016, Scientific Reports.
[89] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[90] Shulei Sun,et al. Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome , 2009, Applied and Environmental Microbiology.
[91] R. E. Lacey,et al. Algal cell rupture using high pressure homogenization as a prelude to oil extraction , 2012 .
[92] Alexander F. Auch,et al. MEGAN analysis of metagenomic data. , 2007, Genome research.
[93] Daniel H Huson,et al. Microbial community analysis using MEGAN. , 2013, Methods in enzymology.
[94] Andreas Wilke,et al. phylogenetic and functional analysis of metagenomes , 2022 .
[95] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[96] Bertil Schmidt,et al. A fast hybrid short read fragment assembly algorithm , 2009, Bioinform..
[97] D. Antonopoulos,et al. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. , 2010, Cold Spring Harbor protocols.
[98] H. Oh,et al. Comparison of several methods for effective lipid extraction from microalgae. , 2010, Bioresource technology.
[99] Davide Heller,et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences , 2015, Nucleic Acids Res..
[100] Tatiana Tatusova,et al. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..
[101] Bahlul Haider,et al. Omega: an Overlap-graph de novo Assembler for Metagenomics , 2014, Bioinform..
[102] Sarah McCalmon,et al. Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene , 2013, Genome research.
[103] A. Sherwood,et al. A molecular method for identification of the morphologically plastic invasive algal genera Eucheuma and Kappaphycus (Rhodophyta, Gigartinales) in Hawaii , 2009, Journal of Applied Phycology.
[104] E. Yang,et al. Evidence of ancient genome reduction in red algae (Rhodophyta) , 2015, Journal of phycology.
[105] Debashish Bhattacharya,et al. Applications of next-generation sequencing to unravelling the evolutionary history of algae. , 2014, International journal of systematic and evolutionary microbiology.
[106] Björn Canbäck,et al. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences , 2008, Bioinform..