⚡♠️ 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

LDPC codes for Illumina sequencing-based DNA storage

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.…

A modernized ART for Illumina read simulation.

Generate simulated illumina sequence reads from a reference sequence

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

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

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

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

📦 Interleave and deinterleave FASTQ files. Streams and gzipped FASTQ files are accepted.

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.