DeepSelecNet is an enhanced deep learning model to perform read classification for selective sequencing.
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Mar 5, 2023 - C
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targeted-sequencing
Here are 20 public repositories matching this topic...
This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm-level copy-number variant calls and arm-level weighted average log2 segment means from segmented copy number data.
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Jan 31, 2024 - R
Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.
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Feb 27, 2024 - Rust
NGSphy: phylogenomic simulation of next-generation sequencing data
coverage next-generation-sequencing read-counts phylogenomics species-trees gene-trees targeted-sequencing
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Mar 9, 2018 - Python
Targeted Amplicon Bisulfite Sequencing Analysis Tool
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May 8, 2019 - Perl
A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
workflow bioinformatics snakemake pipeline ngs public-health metabarcoding ngs-pipeline targeted-sequencing food-monitoring food-authenticity
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Sep 20, 2024 - Python
Identification of gene-fusions, including EML4-ALK
r genetics next-generation-sequencing gene-fusion variant-calling liquid-biopsy bioconductor-package targeted-sequencing circulating-tumor-dna
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May 13, 2025 - R
Create a normalized heatmap for targeted RNAseq count matrix using user-defined housekeeping gene normalization.
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Feb 6, 2020 - R
pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data
bioinformatics genomics mips somatic-variants ngs variants amplicons germline ngstools variant-filtration targeted-sequencing haloplex
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Dec 27, 2022 - Python
data-mining gene-expression kullback-leibler-divergence dimensionality-reduction pharmacogenomics principal-component-analysis breast-cancer targeted-sequencing relative-entropy alzheimers-disease-detection parkinsons-disease-detection finger-prick-blood at-home-testing disease-biomarkers receiver-operating-characteristic-curve differential-distributions toxicology-analysis multivariate-exploratory-data-analysis transcriptomics-markers neurodegeneration-detection
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Aug 7, 2025 - R
A Snakemake pipeline for copy number variant calling without normal tissue samples
bioinformatics snakemake conda cnv bwa panels cna mutect2 targeted-sequencing sequencing-data cnvkit copynumbervariation purecn
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Jul 31, 2025 - Python
Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia
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Feb 22, 2020 - Python
Barcode Analyzer for metabarcoding experiments
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Jun 7, 2021 - Python
For simulations of targeted-sequencing experiments under a known species/gene tree distribution, extracts the reference sequences that be used for mapping.
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Apr 9, 2018 - Python
A detailed bioinformatics workflow for Whole Exome (WES) and Targeted Region Sequencing (TRS) data analysis, covering quality control, alignment, variant calling, annotation, and interpretation using tools like FastQC, Trim Galore, BWA, SAMtools, GATK, and SnpEff.
bioinformatics genomics next-generation-sequencing gatk data-analysis variant-calling wes samtools bwa trs whole-exome-sequencing trimgalore snpeff targeted-sequencing fastqc
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Oct 7, 2025
A Cyrius-based tool for accurate CYP2D6 genotyping from targeted sequencing panels
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Oct 7, 2025 - Python
Coverage analysis of the data from the targeted-sequencing experiment of Hummingbirds (data from the paper Fonseca et al. 2018)
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Sep 12, 2017 - HTML
MSKCC CMO Innovation Lab
python r pipeline makefile perl conda high-performance-computing umi high-throughput-sequencing copy-number-variation targeted-sequencing duplex-sequencing
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May 19, 2023 - Makefile
Tools for analyzing UMIErrorCorrect output
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Nov 14, 2022 - R
🍃 🧬 🧹 Probe set cleaning (Melastomataceae)
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Feb 20, 2024 - Shell
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