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Feb 20, 2023 - Perl
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illumina-sequencing
Here are 46 public repositories matching this topic...
🚀 A sequencing simulator
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Aug 2, 2024 - Python
C++ Library to parse Illumina InterOp files
python csharp cpp python3 interop swig python27 python35 python36 illumina-sequencing python37 python-3-8 python-3-9
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Jul 15, 2024 - C++
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
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Mar 29, 2021 - Perl
A collection of publications on comparison of high-throughput sequencing technologies.
bioinformatics nanopore genomics sequencing pacbio awesome-list genome-sequencing illumina sequence-alignment illumina-sequencing dna-sequencing hifi human-genomes long-read-sequencing
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Jan 2, 2025
Automated pipeline for amplicon sequence analysis
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Dec 4, 2024 - Python
Illumina NovaSeq 6000 server log parsing and analysis for BaseSpace and bcl2fastq pipelines.
ip-address ispconfig illumina csv-export illumina-sequencing illuminate-database log-analytics user-location web-traffic-analysis
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Jan 10, 2025 - Java
LDPC codes for Illumina sequencing-based DNA storage
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Dec 2, 2020 - C
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.…
hts smith-waterman needleman-wunsch heuristics genome-analysis sequence-alignment illumina-sequencing read-mapping nanopore-sequencing hifi-read pacbio-sequencing read-alignments
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Jul 7, 2021 - Jupyter Notebook
Generate simulated illumina sequence reads from a reference sequence
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Dec 21, 2023 - Nextflow
Scripts supporting the manuscript submitted to the Molecular Ecology Resources Special Issue 'Omics for species conservation'
population-genomics illumina-sequencing conservation-genomics oxford-nanopore-sequencing structural-variant-discovery
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Dec 19, 2023 - Shell
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
pipeline metagenomics illumina 16s microbiota illumina-sequencing phyloseq microbial-ecology dada2 16s-seq
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Jun 3, 2024 - R
A modernized ART for Illumina read simulation.
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Jan 23, 2025 - C++
This is the pipeline that handles SARS-CoV-2 samples from the health sector in Region Midtjylland (Illumina PE)
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May 17, 2021 - R
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Jun 15, 2023 - Shell
Detection of Saccharomyces paradoxus DNA across Saccharomyces cerevisiae, and vice versa.
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Jul 25, 2024 - R
Illumina pipeline for 16S sequencing, completed in Python.
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Jul 24, 2017 - Python
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)
incremental fasta fastq-format illumina fastq indels sequence-alignment illumina-sequencing read-mapping spaced-seed simd-intrinsics fasta-format openmp-parallelization sam-file sam-output
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Nov 16, 2017 - C
Discover VNTR-associated DELs that are hard to find using Illumina reads
genomics tandem-repeats sequence-alignment whole-exome-sequencing whole-genome-sequencing illumina-sequencing structural-variation rare-variant-analysis rare-disease
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Jan 17, 2023 - Jupyter Notebook
A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries
variant-calling malaria oxford-nanopore illumina-sequencing amplicon-sequencing plasmodium-falciparum
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Dec 20, 2023 - Python
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