Shotgun metagenomics analysis pipeline for Type 2 Diabetes gut microbiome using Snakemake.
De novo assembly of SARS-CoV-2 genome
MEGAHIT-based de novo assembly of paired-end sequencing data with assembly statistics and contig generation.
A bioinformatic workflow for quality control, read trimming ,read statistics and metagenome assembly using FastQC, fastp, Seqkit and MEGAHIT
A metagenomics pipeline project that runs sequencing QC, taxonomic profiling, assembly, gene prediction, and functional annotation using common CLI tools (FastQC, MetaPhlAn, MEGAHIT, GeneMarkS, BLAST) plus light Python/shell automation.
A reproducible QIIME 2 MOSHPIT pipeline that assembles, bins, dereplicates and taxonomically classifies whole‑metagenome data. Includes MEGAHIT assembly, MetaBAT 2 binning, BUSCO quality control, Sourmash dereplication and Kraken 2/Bracken abundance estimation. Ideal for microbial‑ecology, functional‑genomics and strain‑level profiling studies.
Comparative viromics pipeline designed to profile gut viral communities in neurodysbiosis and control cohorts. Implements de novo MEGAHIT assembly, geNomad prediction, CheckV quality assessment, and Bowtie2 read recruitment to characterize gut bacteriophage signatures in humanized mouse models.
Custom Nextflow scripts for microbiome assembly and AntiSMASH BGC analyses. Based around microbiome assemblers: Megahit & MetaSpades
A genome-resolved metagenomics pipeline replicating the Sharon et al. (2019) gut-brain axis study. Features MEGAHIT de novo co-assembly, Bowtie2 competitive read recruitment, and Anvi'o single-nucleotide variant (SNV) microdiversity profiling.
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