There are 2 repositories under illumina topic.
Viral genomics analysis pipelines
Aligns short reads using dynamic seed size with strobemers
Assembly and intrahost/low-frequency variant calling for viral samples
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Command line utility for manipulating Illumina-generated FASTQ files.
Parse Illumina sample sheets with Python
Demultiplexing pipeline for sequencing data
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.
Explore and download data from the recount3 project
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
A collection of publications on comparison of high-throughput sequencing technologies.
(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
UPHL's Reference Free Pipeline
Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.