Results for "Metagenomics"
Tags
Metagenomics role in antibiotic resistance
Related latest article: http://www.nature.com/nature/journal/v509/n7502/pdf/nature13377.pdfTags: metagenomics, antibiotics resistant, sequencing
3636 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
2870 days ago
- 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
2010 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
1776 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
1428 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
1368 days ago
- 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
1219 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
1112 days ago
ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending cont...Tags: ContigExtender, approach, improve, de novo, sequence, assembly, viral, metagenomics, data
8 days ago
- 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
2830 days ago
