⚡♠️ 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 collection of publications on comparison of high-throughput sequencing technologies.

Automated pipeline for amplicon sequence analysis

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.…

LDPC codes for Illumina sequencing-based DNA storage

Generate simulated illumina sequence reads from a reference sequence

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'

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

Discover VNTR-associated DELs that are hard to find using Illumina reads

Illumina pipeline for 16S sequencing, completed in Python.

Detection of Saccharomyces paradoxus DNA across Saccharomyces cerevisiae, and vice versa.

Illumina (and SOLiD) sensitive read mapping tool (cloned from svn://scm.gforge.inria.fr/svnroot/storm/)

A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries

VIral GEnome ASsembly pipelines for WGS

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