Results for "metagenomics"

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  • Metagenomics role in antibiotic resistance

    Related latest article: http://www.nature.com/nature/journal/v509/n7502/pdf/nature13377.pdf

    Tags: metagenomics, antibiotics resistant, sequencing

    3588 days ago

  • Fancy Oneliner for Bioinformatics !!

    This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder struct...

    Tags: Bioinformatics, Analysis, Visualization, SAM, BAM, Oneliner, NGS, metagenomics

    2822 days ago

  • MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

    MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accele...

    Tags: MEGAHIT, ultra-fast, single-node, solution, large, complex, metagenomics, assembly, succinct, de Bruijn, graph

    1962 days ago

  • Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets

    Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. Developper: Gaëtan Benoit, PhD, former member of the Genscale team at Inria. Contact: claire dot lemaitre at i...

    Tags: Simka, SimkaMin, comparative, metagenomics, method, dedicated, NGS, datasets

    1727 days ago

  • sunbeam: A robust, extensible metagenomics pipeline

    Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin privileges, and can be deployed on most Linux workstations...

    Tags: sunbeam, robust, extensible, metagenomics, pipeline

    1380 days ago

  • SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins

    SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta featur...

    Tags: SqueezeMeta, fully, automated, metagenomics, pipeline, reads, bins

    1320 days ago

  • MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

    MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. Metaeuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to recover optimal exons sets. It reduces redundanc...

    Tags: MetaEuk, sensitive, high-throughput, gene, discovery, annotation, large-scale, eukaryotic, metagenomics

    1170 days ago

  • CoverM: Read coverage calculator for metagenomics

    CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. CoverM calculates coverage of genomes/MAGs coverm genome (help) or individual contigs coverm contig (help). Calculating coverage by...

    Tags: Read, coverage, calculator, metagenomics, CoverM

    1064 days ago

  • Bambus

    Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffold...

    Tags: Scaffolders, Bioinformatics, Assembly, Metagenomics

    2782 days ago

  • Shinyheatmap

    Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well a...

    Tags: Bioinformatics, Analysis, NGS, HeatMap, Genome, Shinyheatmap, R, Visualize, Map, Transcriptomics, Metabolomics, Metagenomics

    2716 days ago