Tag: BUSCO

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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python – samtools and trinity causing inconsistencies in conda env

I’m trying to install busco, detonate, and transrate in conda but I keep getting this error: The environment is inconsistent, please check the package plan carefully The following packages are causing the inconsistency: – bioconda/linux-64::samtools==1.11=h6270b1f_0 – bioconda/linux-64::trinity==2.9.1=h8b12597_0 This is the command I enter conda install -c bioconda busco -y So…

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Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings

Although the hypothesis of gene-regulatory network (GRN) cooption is a plausible model to explain the origin of morphological novelties (1), there has been limited empirical evidence to show that this mechanism led to the origin of any novel trait. Several hypotheses have been proposed for the origin of butterfly eyespots,…

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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

Continue Reading Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

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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Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova

Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…

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Phylogeographic reconstruction of the marbled crayfish origin

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

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Comparative genomics provides insights into the aquatic adaptations of mammals

Species invasions into novel habitats mark major transitions in the evolution of life on Earth. Some of these are relatively ancient, such as the vertebrate transition from the oceans to life on land (∼375 Mya) or the evolution of arboreal vertebrate species (∼160 Mya). When divergent lineages transition to the…

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A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest

1. Edmonds, R. L. & Eglitis, A. The role of the Douglas-fir beetle and wood borers in the decomposition of and nutrient release from Douglas-fir logs. Can. J. Res. 19, 853–859 (1989). Article  Google Scholar  2. Hlásny, T. et al. Living with bark beetles: impacts, outlook and management options. In:…

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

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Whole genome species clustering

I don’t think there is a “best” approach in your situation, given 1) the taxonomy of the group is probably still flaky. 2) being draft genomes, they probably are spotty and have sizeable gaps, and maybe even contaminants. Repeat regions are often left out of such assemblies. Actually, a good…

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BUSCO installation and run

BUSCO installation and run 2 That unil.ch link looks a bit too complicated, these are the commands I ran to get BUSCO via Singularity: Download the image: singularity pull Run the image with example genome.fasta, assuming it’s a genome and a plant: singularity run -B $(pwd):/busco_wd/ busco_v5.2.2_cv1.sif busco -l…

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