Tag: SPAdes

Characterization, genome analysis and genetic tractability studies of a new nanocellulose producing Komagataeibacter intermedius isolate

Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…

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Mobile resistome of microbial communities and antimicrobial residues from drinking water supply systems in Rio de Janeiro, Brazil

Ilyas, M. et al. Environmental and health impacts of industrial wastewater effluents in Pakistan: A review. Rev. Environ. Health 34, 171–186 (2019). MathSciNet  PubMed  CAS  Google Scholar  Roy, M. A. et al. A Metagenomic approach to evaluating surface water quality in Haiti. Int. J. Environ. Res. Public Health 15, 2211…

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Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

Overview of the viromes In all, 41 wild Qinghai voles were collected from pasture habitats located on the eastern Tibetan Plateau, China (Fig. 1). Tissue samples from liver, lung, spleen, small intestine (with content), and feces (large intestinal content) of each vole were disrupted, and viral RNA was extracted. The RNA…

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Genome Assembler for Transcript Assembly

Genome Assembler for Transcript Assembly 2 There are genome assemblers with some kind of –rna or –est options that can be used for transcriptome assembly. MIRA and SPAdes would be in that category, and I am sure there are others. If you are asking if ANY genome assembler can be…

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The genus Serratia revisited by genomics

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

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Index of /~psgendb/birchhomedir/public_html/doc/spades/pyyaml3

Name Last modified Size Description Parent Directory   –   __init__.py 2016-12-30 10:41 9.4K   composer.py 2016-12-30 10:41 4.8K   constructor.py 2016-12-30 10:41 25K   cyaml.py 2016-12-30 10:41 3.2K   dumper.py 2016-12-30 10:41 2.7K   emitter.py 2016-12-30 10:41 42K   error.py 2016-12-30 10:41 2.5K   events.py 2016-12-30 10:41 2.4K  …

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Genetic characterization of two G8P[8] rotavirus strains isolated in Guangzhou, China, in 2020/21: evidence of genome reassortment | BMC Infectious Diseases

Mokomane M, Kasvosve I, Melo Ed, Pernica JM, Goldfarb DM. The global problem of childhood diarrhoeal diseases: emerging strategies in prevention and management. Ther Adv Infect Dis. 2018;5(1):29–43. PubMed  Google Scholar  Organization WH. Rotavirus vaccines: WHO position paper–July 2021. Weekly Epidemiol Rec. 2021;96(28):301–219. Google Scholar  Bucardo F, Reyes Y, Svensson…

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Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS  PubMed  Google Scholar  Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed  PubMed…

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Director of Bioinformatics in Chicago, IL for University of Chicago (UC)

Details Posted: 03-May-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Provides technical expertise in the selection, validation, and implementation of the appropriate internal and external data analytic and bioinformatic solutions needed to analyze specimens, process and integrate data, and…

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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…

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Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology

Stölting KN, Wilson AB. Male pregnancy in seahorses and pipefish: beyond the mammalian model. Bioessays. 2007;29:884–96. PubMed  Google Scholar  Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc. 2020;95:1252–72. PubMed  Google Scholar  Rosenqvist G, Berglund A. Sexual signals and mating…

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Index of /~psgendb/birchhomedir/BIRCHDEV/tutorials/bioLegato/genome_assembly/Assembly

Name Last modified Size Description Parent Directory   –   Assembly.html 2019-11-08 09:20 26K   SOAP-Parameters.png 2019-05-10 07:55 30K   SOAP-addtlLIBS.png 2019-05-09 18:59 110K   SOAPdenovo.log.png 2019-05-10 08:02 31K   abyss.log.png 2019-01-09 14:41 29K   abyss.mate-pair.png 2019-01-08 16:01 15K   abyss.parameters.png 2019-06-10 15:52 15K   abyss_results.png 2019-01-09 14:13 22K  …

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Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics | Environmental Microbiome

Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed  PubMed Central  Google Scholar  Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…

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Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

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Novel gene rearrangement in the mitochondrial genome of Anastatus fulloi (Hymenoptera Chalcidoidea) and phylogenetic implications for Chalcidoidea

1. Osellame, L. D., Blacker, T. S. & Duchen, M. R. Cellular and molecular mechanisms of mitochondrial function. Best Pract. Res. Clin. Endocrinol. Metab. 26, 711–723 (2012). CAS  PubMed  PubMed Central  Google Scholar  2. Bernt, M., Braband, A., Schierwater, B. & Stadler, P. F. Genetic aspects of mitochondrial genome evolution….

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Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

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About QUAST

About Short intro Further reading How to cite Brief project history Authors Funding License and Terms of use Short intro QUAST evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length…

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Index of /~psgendb/doc/bioLegato/blreads

Name Last modified Size Description Parent Directory   –   SOAPdenovo2.hints.html 2019-05-04 15:52 3.9K   Trimmomatic.hints.html 2019-05-20 13:32 6.3K   Trinity.hints.html 2019-04-23 11:39 2.4K   adaptercheck.hints.html 2021-05-13 12:27 8.0K   adaptercheck.html 2021-05-12 17:45 4.9K   adaptercheck_output.png 2021-05-12 17:17 51K   fastq_pair.hints.html 2019-04-05 13:16 3.4K   gffcompare.hints.html 2018-07-18 14:05 3.2K  …

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Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium | BMC Biotechnology

1. Jiang P, Shi FX, Li MR, Liu B, Wen J, Xiao HX, et al. Positive selection driving cytoplasmic genome evolution of the medicinally important ginseng plant genus Panax. Front Plant Sci. 2018;9:359. doi.org/10.3389/fpls.2018.00359. Article  PubMed  PubMed Central  Google Scholar  2. Takeshi T, Marouane B, Takuya I, Kazusato O, Kimiko…

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how to generate reference genome from paired-end reads

how to generate reference genome from paired-end reads 0 Hi, I have a bacteria sample and I want to align this sample to a reference genome. However, a reference genome for this particular strain is not available. So, I need to generate a reference genome from my 2X150 paired-end reads…

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How to execute one command on all files within a directory

How to execute one command on all files within a directory 0 Hi, I have several .fastq (R1 and R2) files in a directory. For example files: 9-Lmm05-P1413070_S9_L001_R1_001.fastq.gz, 9-Lm05-P1413070_S9_L001_R2_001.fastq.gz. I want to run the following command for the all fastq files in the directory and generate separate output directories for…

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Suggestions for Alternate Assembly Resources to Trinity

Suggestions for Alternate Assembly Resources to Trinity 0 As far as I can tell, Galaxy no longer seems to support Trinity as an assembler – or at least, I have not been able to assemble any read data using Trinity for the past several months. Initially, I had had success…

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

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Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS  PubMed  PubMed Central  Article  Google Scholar  2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed  Article  PubMed Central  Google Scholar  3. Borrel G, McCann A, Deane J, Neto…

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Twist Bioscience hiring Bioinformatics Scientist, Production Bioinformatics in South San Francisco, California, United States

Twist is looking for a Bioinformatics Scientist to join our Production Bioinformatics Team. You will work alongside research scientists, software engineers and data scientists to further deliver on our mission to expand access to best-in-class synthetic biology and next-generation sequencing applications. You will be developing and engineering tools to better…

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Hybrid assembly SPAdes (Ox. Nanopore + Illumina)

Hybrid assembly SPAdes (Ox. Nanopore + Illumina) 0 Hi all, I have both Oxford Nanopore and Illumina sequencing data of a bacterial genome. I would like to perform an hybrid assembly combining the two sequencing techniques. Is SPAdes the most appropriate software to do it? And, I typed the following…

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Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

1. Lee, M.-R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638–1646 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Prince, D. S. et al. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 321, 863–868 (1989). CAS  PubMed  Article  Google…

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Assembly with repetitive regions

Assembly with repetitive regions 0 Hello all! I am assembling a synthetic genome sequenced with Oxford Nanopore. The problem is that I obtain a very repetitive assembly with all the contigs such as ATATATATATATATATAT. I do not understand why because I have repeated the process with the Acinetobacter pittii genome,…

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