Metagenomics role in antibiotic resistance
Related latest article: http://www.nature.com/nature/journal/v509/n7502/pdf/nature13377.pdfTags: metagenomics, antibiotics resistant, sequencing
3652 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
2885 days ago
Tags: MEGAHIT, ultra-fast, single-node, solution, large, complex, metagenomics, assembly, succinct, de Bruijn, graph
2026 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
1791 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
1444 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
1384 days ago
Tags: MetaEuk, sensitive, high-throughput, gene, discovery, annotation, large-scale, eukaryotic, metagenomics
1234 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
1128 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
24 days ago
Tags: Scaffolders, Bioinformatics, Assembly, Metagenomics
2846 days ago