Tag: SPAdes

United Nations Inter-agency Group for Child Mortality Estimation. Levels & Trends in Child Mortality: Report 2020, Estimates developed by the United Nations Inter-agency Group for Child Mortality Estimation. New York: United Nations Children’s Fund; 2020. Okomo, U. et al. Aetiology of invasive bacterial infection and antimicrobial resistance in neonates in…

Correa P, Houghton J. Carcinogenesis of Helicobacter pylori. Gastroenterology. 2007;133(2):659–72. Article  CAS  PubMed  Google Scholar  Dube C, Tanih N, Ndip R. Helicobacter pylori in water sources: a global environmental health concern. Rev Environ Health. 2009;24(1):1–14. Article  CAS  Google Scholar  Stark RM, Gerwig GJ, Pitman RS, Potts LF, Williams NA, Greenman…

Adamek, M., Spohn, M., Stegmann, E. & Ziemert, N. Mining bacterial genomes for secondary metabolite gene clusters. Methods Mol. Biol. 1520, 23–47 (2017). CAS  PubMed  Google Scholar  Belknap, K. C., Park, C. J., Barth, B. M. & Andam, C. P. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces…

Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article  PubMed  PubMed Central  Google Scholar  Bankevich A, Nurk S,…

Kiu, R. & Hall, L. J. An update on the human and animal enteric pathogen Clostridium perfringens. Emerg. Microbes Infect. 7, 141 (2018). Article  PubMed  PubMed Central  Google Scholar  Li, J., Paredes-Sabja, D., Sarker, M. R. & McClane, B. A. Clostridium perfringens sporulation and sporulation-associated toxin production. Microbiol. Spectr. doi.org/10.1128/microbiolspec.TBS-0022-2015…

Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, et al. The population biology of invasive species. Annu Rev Ecol Syst. 2001;32:305–32. Article  Google Scholar  Allendorf FW, Lundquist LL. Introduction: population biology, evolution, and control of invasive species. Conserv Biol. 2003;17:24–30. Article  Google Scholar  Erickson AB. The…

Elmore, S. Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495–516 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  Shi, Y. Caspase activation, inhibition, and reactivation: A mechanistic view. Protein Sci. 13, 1979–1987 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  Alberts, B., Johnson, A. & Lewis, J….

How to align Illumina FASTQ isolates to a conserved gene for phylogenetic analysis 0 I am currently working on a project involving 100 isolates in Illumina FASTQ format. The objective of my study is to investigate the phylogenetic relationships among these isolates based on a conserved sequence within the HMG…

Chenxing Wei,1,* Jian Chen,1,* Tanveer Muhammad Anwar,2,* Lingling Huang,1 Wenjie Yang,3 Xueyan Dong,1 Qiong Chen,1 Min Yue,2,4,5 Daojun Yu1,3 1Department of Medical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China; 2Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University…

How could I filter a metagenomic assembly file (from Megahit or metaspades) for low coverage/short contigs to enable faster downstream analysis (i.e blastn) 0 Title is pretty selg-explanatory, can i filter down a de-novo metagenomic assembly to make downstream analysis like blastn run faster? metagenomics blast spades megahit assembly •…

Feldhaar H. Bacterial symbionts as mediators of ecologically important traits of insect hosts. Ecol Entomol. 2011;36:533–43. Article  Google Scholar  Douglas AE. Symbiosis as a general principle in eukaryotic evolution. Cold Spring Harb Perspect Biol. 2014;6:a016113–a016113. Article  PubMed  PubMed Central  Google Scholar  Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. Defensive…

Reconstruction of gene and macro-synteny trees for the three studied Papaver species Syntenic blocks within the three Papaver species were identified with OrthoFinder v2.3.15. Orthologous and paralogous relationships, as well as orthogroups, were inferred using the parameters “-M msa -T fasttree” based on proteome sequences from multiple species. The resulting…

Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, et al. Complete nitrification by Nitrospira bacteria. Nature 2015;528:504. Article  CAS  PubMed  PubMed Central  Google Scholar  van Kessel MA, Speth DR, Albertsen M, Nielsen PH, den Camp HJO, Kartal B, et al. Complete nitrification by a single microorganism….

AttributeError: module ‘collections’ has no attribute ‘Hashable’ 0 Hello everyone I’m new using Spades and today I’m trying to do an assembly but I have a problem when I try to execute the pipeline. This is my script: spades.py -1 B_cepacia_raw_R1_paired.fastq.gz -2 B_cepacia_raw_R2_paired.fastq.gz -o spades_error_corrected_reads -t 50 -m 500 –only-error-correctio…

Suttle, C. A. Environmental microbiology: Viral diversity on the global stage. Nat. Microbiol. 1, 16205 (2016). Article  CAS  PubMed  Google Scholar  Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436 (2020). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Dutilh, B. E., Reyes,…

Mason-D’Croz, D. et al. Modelling the global economic consequences of a major African swine fever outbreak in China. Nat. Food 1, 221–228 (2020). Article  PubMed  PubMed Central  Google Scholar  Sehl, J. et al. Comparative pathology of domestic pigs and wild boar infected with the moderately virulent African swine fever virus…

Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123–140 (2004). Article  CAS  PubMed  Google Scholar  Nataro, J. P. & Kaper, J. B. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11, 142–201 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  Croxen, M. A….

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51. Article  CAS  PubMed  PubMed Central  Google Scholar  Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, et al. Evolutionary relationships of wild hominids recapitulated…

Hi, I’m new to this field, having only few experience of reference mapping once in my bachelor years. I am trying to do a QTL analysis of a population of plants derived from two parents. Since this specie is lacking the stable reference genome, I’m trying to build a new…

Genetic Variation studies often involve analyzing samples from a previously studied species. For instance, it is of interest to examine genomes of various cultivars, strains, or populations of the same species. In such cases, it may be necessary to perform de novo DNA-Seq assembly to obtain the genome of the…

Crous, P. et al. Fungal planet description sheets: 107–127. Pers. Mol. Phylogeny Evol. Fungi 28, 138–182. doi.org/10.3767/003158512X652633 (2012). Article  CAS  Google Scholar  Visentin, I. et al. Gnomoniopsis castanea sp. nov. (Gnomoniaceae, Diaporthales) as the causal agent of nut rot in sweet chestnut. J. Plant Pathol. 94, 411–419. doi.org/10.4454/JPP.FA.2012.045 (2012). Article …

Conda is installing older version of Spades even though latest version is there in the bioconda repository 1 I am trying to install spades using conda. Even though the bioconda has the latest version, the version getting installed in my system is an older version 3.13. Initially, I thought creating…

Willing, B. P. et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844–1854 (2010). Article  PubMed  Google Scholar  Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012)….

Figure 1a provides an overview of the experimental procedure and it is summarized in the following sections. Fig. 1: Schematic overview of high-resolution optical DNA mapping-based bacterial typing. a Experimental pipeline. The DNA, extracted via plug-lysis, is labelled with YOYO-1 and netropsin in a single step. The DNA is confined to…

Introduction Over the last decades, Proteus species infections have received special attention because of the emergence of some species resistant to various antimicrobial agents, particularly β-lactams.1 Proteus penneri, first recognized in 1982, is a member of the Enterobacteriaceae family, which is salicin- and esculin-negative and chloramphenicol-resistant.1,2 P. penneri is primarily…

Forum:Small viral contigs in denovo assembly using spades 0 Dear All, I am trying spades to perform de novo assembly for my viral genomes. Unfortunately, these viral genomes have no references to compare with. For some of the samples, I got 40kb to 90kp contigs. But for some, I get…

forcing read error correction using SPAdes 2 Given that this is my code below, why is SPAdes giving me the following message?: Mode: ONLY assembling (without read error correction) Debug mode is turned OFF I would like for the assembly to complete the read error correction step if possible. Based…

mapping or denovo assembly of genome with big diversity (Chlamydomonas)? 0 I have question, as this is usually not my field of working at all! I’m used to work with bacterial genomes, but I have small project including Chlamydomonas mutants then I would like to ask experts what they are…

Recreating a SPAdes Assembly 0 Hi. I created a metagenome assembly using SPAdes, mapped the assembly using Bowtie2 and Samtools (creating BAM and the indexed BAI files), then binned the assemblies. Somewhere in the file back-up process the SPAdes assembly file was over written. I’d like to recreate my SPAdes…

How do we know that the AMR genes/ MGEs in the contig sequence is on plasmid or Chromosome? 0 Hi everyone, I have a set of bacterial contigs genomes generated by Spades assembler. I am trying to find the method for identifying whether the contig sequence is a plasmid or…

P. aeruginosa bacterial strains Reference strains Four well-described and genome-available reference strains were used in the present study, ATCC27853 and ATCC15442, obtained from the American Type Culture Collection (ATCC), and PAO1 and PA14, from the collection of Institut Pasteur (Paris, France). Strain ATCC15442 is recommended for disinfectant susceptibility testing44, strain…

comparing two metagenomics data sets 2 Hello all, I have a shotgun metagenomic dataset (20 samples) paired-end reads. I want to compare my data to another dataset published and available online. I am confused as how can I do it. Please let me know if you have an idea. Thanks…

Andersen LO, Bonde I, Nielsen HB, Stensvold CR. A retrospective metagenomics approach to studying Blastocystis. FEMS Microbiol Ecol. 2015. doi.org/10.1093/femsec/fiv072. Article  Google Scholar  Audebert C, Even G, Cian A, Loywick A, Merlin S, Viscogliosi E, et al. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human…

Orcutt B, D’Angelo T, Jungbluth SP, Huber JA, Sylvan JB. Microbial life in oceanic crust. OSF Preprints, 2020; doi.org/10.31219/osf.io/2wxe6. Koonin EV. On the origin of cells and viruses: primordial virus world scenario. Ann NY Acad Sci. 2009;1178:47–64. Nigro OD, Jungbluth SP, Lin HT, Hsieh CC, Miranda JA, Schvarcz CR, et…

Contributed Commentary by Mladen Lazarevic, Seven Bridges  February 3, 2023 | Researchers turn to bioinformatics computing to analyze large datasets and tackle issues ranging from precision medicine solutions in oncology to novel drug therapies. This is especially true of genomic data and bioinformatics analysis.   While those in the life sciences…

Koonin, E. V. & Dolja, V. V. Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol. Mol. Biol. Rev. 78, 278–303 (2014). Article  CAS  Google Scholar  Pritham, E. J., Putliwala, T. & Feschotte, C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and…

Singh, J. S. The biodiversity crisis: A multifaceted review. Curr. Sci. 82(6), 638–647 (2002). Google Scholar  Mateo-Tomás, P. & López-Bao, J. V. A nuclear future for biodiversity conservation?. Biol. Conserv. 270, 109559. doi.org/10.1016/j.biocon.2022.109559 (2022). Article  Google Scholar  Humphreys, A. M., Govaerts, R., Ficinski, S. Z., Nic Lughadha, E. & Vorontsova,…

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,…

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…

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…

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…

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….

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  …

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…

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…

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…

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…

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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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…

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…

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….

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…

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…

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  …

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…

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…

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…

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…

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…

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…

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…

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…

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…

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,…