Pinned Repositories
amr-profiler
Snakemake workflow to characterize the presence and abundance of antibiotic resistance genes in metagenomic datasets.
genofan
Workflow for functional annotation of a set of bacterial genomes
gubascreen
Protocol for detecting Gubaphage genomes among a set of predicted viral sequences
lab-website-template
(Pre-release) An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more
latinbiota
Central repository with scripts and workflows for the analysis of the gut microbiome of the Latinbiota cohort
magscreen
Snakemake workflow to screen a set of genomes (e.g., MAGs) against an existing genome database and identify novel species
metamap
Snakemake workflow to map and quantify microbial genomes in metagenomic reads
ml-microbiome
Snakemake workflow to perform machine learning classification of microbiome sequence data
protean
Workflow for functional annotation of large collections of protein sequences
virsearch
Snakemake workflow to detect and classify viruses in metagenome assemblies.
alexmsalmeida's Repositories
alexmsalmeida/virsearch
Snakemake workflow to detect and classify viruses in metagenome assemblies.
alexmsalmeida/metamap
Snakemake workflow to map and quantify microbial genomes in metagenomic reads
alexmsalmeida/magscreen
Snakemake workflow to screen a set of genomes (e.g., MAGs) against an existing genome database and identify novel species
alexmsalmeida/ml-microbiome
Snakemake workflow to perform machine learning classification of microbiome sequence data
alexmsalmeida/amr-profiler
Snakemake workflow to characterize the presence and abundance of antibiotic resistance genes in metagenomic datasets.
alexmsalmeida/genofan
Workflow for functional annotation of a set of bacterial genomes
alexmsalmeida/latinbiota
Central repository with scripts and workflows for the analysis of the gut microbiome of the Latinbiota cohort
alexmsalmeida/protean
Workflow for functional annotation of large collections of protein sequences
alexmsalmeida/gubascreen
Protocol for detecting Gubaphage genomes among a set of predicted viral sequences
alexmsalmeida/lab-website-template
(Pre-release) An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more
alexmsalmeida/Metagen-FastQC
Wrapper to clean metagenomic reads
alexmsalmeida/metagen-fetch
Snakemake workflow to download and process public metagenomic sequence datasets
alexmsalmeida/mlst-profiler
Snakemake workflow to profile the MLST of known bacteria in metagenomic data
alexmsalmeida/Tax-Benchmarking
Benchmarking taxonomic analysis tools and databases.