⚡♠️ 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

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

Illumina pipeline for 16S sequencing, completed in Python.

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

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/, original code from @marta- , with some work done by @yoann-dufresne)

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

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