Welcome to sieve’s documentation!
SIEVE is a bioinformatic step-wise analysis pipeline for assembly, binning and annotation of metagenomes from MGNify API (EBI) or local user data. Sieve is a Nextflow pipeline very easy to use and offers a simple and intuitive interface to see your results.
Check out the Usage section for further information, including how to installation the project.
Note
This project is under active development.
Contents
- Introduction
- Installation
- Invoking sieve
- Do you want to reconstruct MAGs from a specific sample?
- Do you want to reconstruct MAGs from a specific organism?
- Do you want to reconstruct MAGs by looking for specific genes?
- Do you want to reconstruct MAGs by looking for macromolecular system? Pathways?
- Do you want to reconstruct MAGs using specific binning algorithm and quality criteria?
- Do you want to use local and public metagenomes?
- Usage
- Parameters
- Output
- Introduction
- Pipeline overview
- Control of local input reads
- Fetching data from MGnify API
- Identification of genes of interest
- Assembly
- Gene prediction
- Identification of macromolecular systems
- Taxonomic classification of the targeted contigs
- Binning and binning refinement
- Genome annotation of binned genomes
- Taxonomic classification of binned genomes
- Summary