muneebdev7
Muneeb Nasir
First release of MetaBolt⚡, an end-to-end, fully automated Nextflow pipeline that accelerates the recovery of metagenome-assembled genomes (MAGs) from raw metagenomic reads.
This release of pipeline integrates a novel, optimized k-mer strategy to significantly improve assembly efficiency, allowing for rapid, reproducible, and accurate recovery of MAGs from complex microbial communities.
Key Features
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Optimized de novo metagenome assembly (MEGAHIT) with a reduced k-mer set for faster and more efficient genome reconstruction.
- Checkout our study of optimization of assembly: https://www.biorxiv.org/content/10.1101/2024.06.08.598064v2.full.pdf
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Fully automated MAG recovery from raw reads to classified bins
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Parallelized, modular workflow built with Nextflow DSL2 for scalability and maintainability
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Preprocessing & QC:
- Quality assessment using FastQC
- Adapter trimming and filtering via fastp
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Assembly & Mapping:
- High-performance assembly with MEGAHIT
- Read alignment using BWA-MEM and SAMtools
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Genome Binning:
- MAG reconstruction with MetaBAT2
- Depth profiling using jgi_summarize_bam_contig_depths
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Reporting & Summaries:
- Aggregated workflow summary via MultiQC
- DAG visualization, trace reports, and software version logs
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Sustainability Reporting:
- Carbon footprint estimation with nf-co2footprint plugin
Author
Full Changelog
For detailed changes, improvements, and fixes, see the CHANGELOG.md