illumina-sequencing
There are 38 repositories under illumina-sequencing topic.
tseemann/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
HadrienG/InSilicoSeq
:rocket: A sequencing simulator
Illumina/interop
C++ Library to parse Illumina InterOp files
rhshah/IMPACT-Pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
Nazeeefa/awesome-sequencing-tech-papers
A collection of publications on comparison of high-throughput sequencing technologies.
AlejandroAb/CASCABEL
Automated pipeline for amplicon sequence analysis
Mangul-Lab-USC/review-technology-dictates-algorithms
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.org/abs/2003.00110.
shubhamchandak94/LDPC_DNA_storage
LDPC codes for Illumina sequencing-based DNA storage
BCCDC-PHL/simulate-short-reads
Generate simulated illumina sequence reads from a reference sequence
Headonpillow/16S_analysis
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
janawold1/2023_MER_Special_Issue
Scripts supporting the manuscript submitted to the Molecular Ecology Resources Special Issue 'Omics for species conservation'
cmkobel/pipe19
This is the pipeline that handles SARS-CoV-2 samples from the health sector in Region Midtjylland (Illumina PE)
ColleenBobbie/Illumina-pipeline
Illumina pipeline for 16S sequencing, completed in Python.
kevin-wamae/PlasmoSeq-DualTech
A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries
khourious/vigeas
VIral GEnome ASsembly pipelines for WGS
laurentnoe/storm
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)
nicolo-tellini/intropipeline
Detection of Saccharomyces paradoxus DNA across Saccharomyces cerevisiae, and vice versa.
petermchale/trfermikit
Discover VNTR-associated DELs that are hard to find using Illumina reads
adrianagiongo/RhizoWheat-ms1
Workflow and R scripts for Giongo et al. (2024)
AwesomeTimeTraveler/IntegrativeMultiOM
IMOM - A pipeline for interacting with, processing, and analyzing multi-OM datasets in phylogenetic and evolutionary context
CSynodinos/illumina-cnv-vcf-analyzer
Copy Number Variant Analyzer for Illumina Dragen files. Work in Progress...
darakibr/GBS
Group B Strep pipelines for large dataset gene analysis from Illumina sequencing.
ebewo/LpSIM
LpSIM is a virtual platform for simulating the different stages of the Illumina sequencing library preparation workflow and the possible artefacts that may be introduced at each stage.
guillaume-gricourt/HmnIllumina
Parse Illumina InterOp folder
Louise-la/RNA_seq_alignment_pipeline
RNA-Seq Pipeline for processing paired-end FASTQ transcripts generated from Illumina sequencing. The pipeline trims adapter sequences, aligns transcripts to a specified region of interest on the reference genome, and facilitates downstream analysis.
nicolo-tellini/ils-pipeline
ABBA-BABA test conducted on Saccharomyces cerevisiae strains using whole-genome alignment.
wennj/plasmid-collapse-gene-loss-unicycler-galaxy
Accompanying information to a scientific publication on the assembly of bacterial genomes using Illumina and nanopore sequencing data using Unicylcer.
BCCDC-PHL/symlink-seqs
Create fastq symlinks for selected samples in sequencer output directories based on several criteria
FabbriniMarco/Generate-MiSeq-Manifest
Generate a .CSV manifest file for importing multiple samples in the Illumina MiSeq machine
gauravcodepro/alignments-code-generator
code getter for illumina, pacbio, oxford long reads alignments.
gauravcodepro/miseq-nextseq-novaseq-genome
genome assembler for cleaning, mapping and assembling genomes.
JazzEd-EdTech/action-build
A Github action for building Snapcraft projects
quadram-institute-bioscience/interleafq
📦 Interleave and deinterleave FASTQ files. Streams and gzipped FASTQ files are accepted.
YU-Zhejian/art_modern
A modernized ART for Illumina read simulation.