![]() Recovery of prokaryotic genomes from shotgun metagenomic sequencing data More scalable dereplication for metagenome assembled genomesīioinformatics tool outputs converter to JSON or YAML Scales to >1M cells.Ĭode examples of fast and simple k-mer counters for tutorial purposesĪ versatile pairwise aligner for genomic and spliced nucleotide sequences This package contains deep learning models and related scripts for RoseTTAFoldĪRCTool is a Python script to extract RARC, Yaz0, and U8 archives. Phylogenetic placement and downstream analysisĪ genomic minhashing implementation in Rust Documentation:ĪGREDA (AGORA-based REconstruction for Diet Analysis) is a new repository of genome-scale metabolic models of human gut microbes.ĭeblur is a greedy deconvolution algorithm based on known read error profiles.Ī Python package for microbiome sequencing analysis with QIIME 2 ![]() The COnstraint-Based Reconstruction and Analysis Toolbox. GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network). Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly This is the development home of the workflow management system Snakemake. Official repository for the QIIME 2 framework. Quick summary statistics on fasta/fastq(.gz) filesĪn example using custom theme in a Beamer presentation using R Markdown (pdf format) VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies Source code and demos for "Rapid identification of pathogenic bacteria using Raman spectroscopy and deep learning" Visualization and Analysis of mass spectrometric and chromatographic data.Ĭode for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"Ī fast and scalable phylogenetic tree viewer for microbiome data analysis Software library for Maldi-Tof preprocessing and machine learning analysis. Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models. Parse multiple Antimicrobial Resistance Analysis Reports into a common data structureĪ free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods.Īntimicrobial Resistance Identification By Assembly :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes ![]() MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read Metagenomics MetaFlow is a program for community profiling of a metagenomic sample Supporting code for uncultivated gut virus manuscript Profiling of Human Gut Virome with Oxford Nanopore Technology Calculating and Visualizing ROC and PR Curves Across Multi-Class Classifications ![]()
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