RGFA: powerful and convenient handling of assembly graphs
...h the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed u...1576 days ago
2191 days ago
ASAR: Advanced metagenomic Sequence Analysis in R
An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on K...2136 days ago
CLARK: Fast, accurate and versatile sequence classification system
...bsp;k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial geno...1550 days ago
Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
...ates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak...oftware suite will perform various steps in metagenomic analysis workflows including...eproducibility. More at https://dahak-metagenomics.github.io/dahak/1496 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,...1426 days ago
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
...ny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS...rmatics treatment of raw reads for targeted metagenomics, statistical analysis and re...MAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom)...1366 days ago
mixtureS: a novel tool for bacterial strain reconstruction from reads
mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 24...1362 days ago
1216 days ago
Tiara: deep learning-based classification system for eukaryotic sequences
With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of eukaryotic diversity.791 days ago