borenstein-lab / fishtaco
FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of microbiome functional shifts
☆24Updated 3 years ago
Alternatives and similar repositories for fishtaco:
Users that are interested in fishtaco are comparing it to the libraries listed below
- Metagenomic species profiling with enhanced coverage of the human gut microbiome☆25Updated 10 months ago
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host…☆21Updated last year
- Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation☆29Updated 3 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.☆15Updated 3 years ago
- ☆22Updated 2 years ago
- A Shotgun Metagenome Annotation Pipeline☆23Updated 8 years ago
- Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles☆35Updated last year
- Tools for extracting individual genomes from metagenomes☆17Updated last year
- OPAL: Open-community Profiling Assessment tooL☆28Updated 3 months ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 3 years ago
- Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs☆18Updated 3 years ago
- Reference Phylogeny for Bacterial and Archaeal Genomes☆25Updated 2 years ago
- Utility program for extracting sequences from a fasta/fastq file☆36Updated 3 months ago
- Strain Prediction and Analysis with Representative SEquence☆18Updated 4 months ago
- Advanced metagenomic Sequence Analysis in R☆15Updated 6 years ago
- Annotate sequences from BLAST against KEGG DB with KO numbers and summarize them in KEGG modules.☆22Updated 6 years ago
- Toolkit for establishing, updating, and validating GTDB species clusters☆20Updated last week
- A repository with scripts to run pipeline that are commonly used in the Meren Lab☆11Updated 7 years ago
- Extract lineage CSVs from NCBI for use with sourmash lca.☆28Updated last year
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…☆25Updated 2 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 7 years ago
- Phasing for metagenomics using PacBio long reads☆17Updated 3 years ago
- Calculates the lowest common ancestors of each query sequence in a Blast result☆31Updated 7 years ago
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated last year
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆17Updated last year
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- MAG Circularization Method☆33Updated 2 years ago