- 🎯 Overview
- 🔍 Features
- 🛠 Prerequisites
- 📥 Installation
- 🚀 How to Run
- ⚙️ Arguments
- 🔏 License
- 🖊️ Citing minMutFinder
- 🔮 Future Work & Limitations
- ✉️ Get in Touch
- 📚 References
minMutFinder is a bioinformatics tool designed to help you identify minority mutations in population variants with precision and accuracy. Unlike other tools, minMutFinder considers the possibility of multiple nucleotide mutations within the same codon and provides comprehensive metrics for your sequences.
- 🧬 Advanced Mutation Detection: Identifies minority mutations while accounting for multiple nucleotide changes within a single codon.
- 📊 Comprehensive Analysis: Provides detailed metrics and plots for a thorough understanding of your sequences.
- 🔧 Customizable: Supports various versions and annotated mutations for enhanced flexibility.
Ensure the following programs are installed:
| Software | Version | Installation |
|---|---|---|
| Nextflow | 23.10.1 or higher | Install |
| Python | 3.9 | |
| libgcc-ng | 12 or higher | conda-forge |
| Trimmomatic | 0.39 | Bioconda |
| Minimap2 | 2.26 | Bioconda |
| Lofreq | 2.1.5 | Bioconda |
| Bcftools | 1.17 | Bioconda |
| Samtools | 1.17 | Bioconda |
os, pandas, sys, csv, gzip, shutil, matplotlib, seaborn, Bio, re, plotly, numpygit clone https://github.com/ValldHebron-Bioinformatics/minMutFinder.git
cd minMutFinder# Install conda-forge dependencies
conda install -c conda-forge libgcc-ng>=12
# Install bioconda dependencies
conda install -c bioconda minimap2=2.26 htslib=1.17 bcftools=1.17 samtools=1.18 trimmomatic=0.39 lofreq=2.1.5=py39hb7ef6d5_10
# Install Python dependencies
pip install pandas>=2.1.4 Bio>=1.5.9 plotly>=5.18.0 numpy>=1.26.2 pysam>=0.21.0 matplotlib>=3.8.2 seaborn>=0.13.0nextflow run minMutFinder.nf --ref_seq <reference.fasta> --out_path <output_name> --r1 <forward_reads.fastq.gz> --r2 <reverse_reads.fastq.gz> --annotate <mutations.tsv> --syn_muts <"yes"/"no">--ref_seq: Path and filename of the reference genome FASTA file (1)(2)(4)--out_path: Output name for the virus column--r1: Path and filename of the forward FASTQ compressed file--r2: Path and filename of the reverse FASTQ compressed file--annotate: Path and filename of the TSV file containing the annotated mutations (3)--syn_muts: "yes" or "no", depending on whether to include synonymous mutations in the output plot (default is "no")
- The reference genome must contain the coding sequences (CDS) of the proteins. If there are multiple proteins, they should be separated in the FASTA file.
- FASTA headers must use underscores (
_) between words. For example:>NC_006273_2_UL96. - The annotated mutation file should be tab-separated and contain a column named
mutationfor annotated mutations. - If FASTA headers share patterns (e.g. H3N2_PA and H3N2_PA_X share H3N2_PA) they must be differentiated (e.g. H3N2_PA_prot, H3N2_PA_X).
This project, minMutFinder, is licensed under the GNU General Public License v3.0. You are free to use, modify, and distribute this software under the terms of this license. For more details, refer to the LICENSE file.
A research paper on minMutFinder is currently in progress. In the meantime, please cite this GitHub repository using the citation provided by GitHub. You can find the official citation by clicking the "Cite this repository" button at the top of the repository page or view the citation file directly.
- As of now, minMutFinder has only been tested on viral sequencing data.
- Only available for Illumina® sequencing data.
- Allele Frequency (AF) ≥ 5%
- Read depth per nucleotide position ≥ 20
- Number of threads = 64
- At the moment we are working on uploading minMutFinder to nf-core, for easier distribution and use.
- Support for user-provided VCF files along with SAM/BAM files, skipping the initial quality control, mapping, and variant calling steps.
- Make it possible for the user to choose the number of threads, AF, Read depth per nucleotide positon.
- Make it possible for the user to choose kind of output desired (complete or just final result files).
- Support for ONT® sequencing data.
If you encounter any issues, have feature requests, or need assistance, feel free to reach out:
- Open an issue directly in this repository by clicking here.
- Email us at ignasi.prats@vhir.org.
We're always happy to help!