Allows users to study microbial communities. DEMIC can infer the relative distances of contigs from the replication origin and compare bacterial growth rates between samples. It was used to estimate the growth rates in over 120 species-experiment combinations. This tool performs growth estimation based on principal component analysis (PCA) of contig coverages in multiple samples.
Analyzes the time series data of microbial community profiles. MetaMIS is based on a Lotka-Volterra model and can interpret interaction networks. It works well with high level of missing data and the influence of rare microbes is ignored to estimate interaction information. The tool can be used in comparative studies thank to its capability to organize multiple interaction networks into a consensus network. It allows researchers to analyse interactive relations conveniently and to visualize network topology.
Maps reads to a closed reference of peptides. FAMLI provides an algorithmic method dedicated to the assignment of whole genome sequencing (WGS) reads to the appropriate reference sequence. FAMLI is an open source package that can be used for determining protein-coding sequences related with disease from human microbiome samples or being used in conjunction with other tools to increase their precision.
Creates sample identifiers that is unique across projects, project teams, and institutions with some properties: short; correctable with respect to common types of transcription errors; opaque and compatible with existing standards without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers (UUIDs), that are globally unique to their samples. It generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project.
Aims to compute a succinct index data structure in linear time. Spacegraphcats is a scalable graph query framework that exploits the structural sparsity of compact De Bruijn assembly graphs. This method supports alternative approaches such as querying with k-mers belonging to genes of interest. It can also be applied in metagenomics fields such as developement of metrics for genome binning quality, analysis of pangenome neighborhood structure, and investigation of de novo extraction of genomes based on neighborhood content.
Analyzes metagenomes and discovers fold hits associated to a target protein structurally characterized and with a determined activity. MetaFoldScan allows the identification of structural homologs and accordingly biologically relevant enzymes in ecological system such as human gut microbiota. It permits intensive and robust screening of meta-data to find structural homologs of target proteins.