Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination
☆14Sep 1, 2025Updated 5 months ago
Alternatives and similar repositories for preprocessing
Users that are interested in preprocessing are comparing it to the libraries listed below
Sorting:
- ☆12Apr 6, 2021Updated 4 years ago
- This repo is designed as a step-by-step tutorial to teach RNA-seq analysis☆16Dec 21, 2025Updated 2 months ago
- Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles☆43Mar 26, 2024Updated last year
- Analysing Metagenomic Species (MGS)☆42Nov 12, 2020Updated 5 years ago
- The seqtime R package provides functions to analyse sequencing data time series and to simulate community dynamics☆21Dec 9, 2022Updated 3 years ago
- Chang and Gupta et al., Gut Microbiome Wellness Index 2 Enhances Health Status Prediction from Gut Microbiome Taxonomic Profiles, Nature …☆25Jan 20, 2025Updated last year
- CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data☆27Feb 20, 2026Updated last week
- Re-analysis of data provided by Gihawi et al. 2023 bioRxiv☆26Aug 8, 2023Updated 2 years ago
- This repo collects the list of podcasts related to microbiome science: science, microbiology and bioinformatics.☆31Jan 28, 2026Updated last month
- Genomic sequence aligner☆33Oct 21, 2025Updated 4 months ago
- Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.☆143Dec 17, 2025Updated 2 months ago
- ☆34Sep 5, 2024Updated last year
- A metagenomic and isolate assembly and analysis pipeline built with AMOS☆93Nov 20, 2017Updated 8 years ago
- Analysis framework for integrating gut microbiome and host gene expression data☆35Apr 25, 2022Updated 3 years ago
- ALDEx_bioc is the working directory for updating bioconductor☆30May 1, 2025Updated 9 months ago
- MethyLYZR: a Naïve Bayesian framework for rapid brain tumor classification from sparse epigenomic data☆16Mar 3, 2025Updated 11 months ago
- Course materials for the Advanced Courses Working With Pathogen Genomes course run virtually in Asia 10-14 May 2021☆10Jul 5, 2024Updated last year
- ☆12Feb 26, 2019Updated 7 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆39Sep 17, 2025Updated 5 months ago
- ☆40Dec 16, 2023Updated 2 years ago
- An open-source redundant distributed storage network☆17Oct 3, 2014Updated 11 years ago
- Snakemake workflow to map and quantify microbial genomes in metagenomic reads☆13Oct 10, 2025Updated 4 months ago
- Compute strain abundance in a defined microbial community☆10Jul 27, 2023Updated 2 years ago
- 16S rRNA Sequencing Data from the Human Microbiome Project☆10Oct 30, 2025Updated 4 months ago
- ☆11Apr 5, 2021Updated 4 years ago
- Application of deep generative model discovers novel and diverse functional peptides against microbial resistance☆11Dec 22, 2022Updated 3 years ago
- Command line client and Python libraries for CosmosID API☆12Oct 28, 2025Updated 4 months ago
- A Python+Web tool visualizes ward placements and smoke usage from professional matches using DOTABUFF data. It creates interactive heatma…☆22Nov 16, 2025Updated 3 months ago
- ☆11Feb 9, 2024Updated 2 years ago
- ☆10Nov 24, 2019Updated 6 years ago
- MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data☆13Jan 28, 2026Updated last month
- A repository for large-scale microbiome datasets, formatted for phyloseq☆40Apr 8, 2024Updated last year
- A visualization tool for exploratory data analysis of metagenomic data☆39Mar 22, 2022Updated 3 years ago
- Code used in MiCE 8992 Spring 2016☆44Apr 19, 2016Updated 9 years ago
- Antimicrobial Peptide Structural Evolution Miner (AMP-SEMiner), an integrated AI framework designed for the simultaneous identification o…☆13May 10, 2025Updated 9 months ago
- Reference-free quality assessment for Hi-C sequencing data☆13Apr 30, 2024Updated last year
- WARNING: This repository is no longer maintained ⚠️ This repository will not be updated. The repository will be kept available in read-on…☆11Nov 15, 2017Updated 8 years ago
- A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments☆11Dec 1, 2020Updated 5 years ago
- MaAsLin3: Microbiome Multivariate Association with Linear Models☆69Updated this week