illumina-sequencing

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

🚀 A sequencing simulator

C++ Library to parse Illumina InterOp files

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

A modernized ART for Illumina, MGI Tech & More read simulation.

A collection of publications on comparison of high-throughput sequencing technologies.

LDPC codes for Illumina sequencing-based DNA storage

Automated pipeline for amplicon sequence analysis

Illumina NovaSeq 6000 server log parsing and analysis for BaseSpace and bcl2fastq pipelines.

A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.…

Generate simulated illumina sequence reads from a reference sequence

High-performance Julia tool for sequence demultiplexing

A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

Scripts supporting the manuscript submitted to the Molecular Ecology Resources Special Issue 'Omics for species conservation'

Series of scripts to analyse 454 and Illumina sequences in SSU amplicon against MaarjAM database

A modular Nextflow-based pipeline for efficient analysis of Illumina short-read metagenomic data, supporting both rapid read-level profiling and genome-resolved assembly, with a focus on accessibility, epidemiological surveillance, and reliable performance on resource-limited systems.

A Nextflow shotgun metagenomics pipeline with Illumina reads. / Pipeline Nextflow de métagénomique de type shotgun avec des séquences Illumina.

A scalable Nextflow pipeline for automated WGS analysis, optimized for Oxford Nanopore and hybrid ONT–Illumina assemblies in clinical microbiology research.

This is the pipeline that handles SARS-CoV-2 samples from the health sector in Region Midtjylland (Illumina PE)