cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
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Aug 18, 2022 - Python
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snv
Here are 24 public repositories matching this topic...
Generic human DNA variant annotation pipeline
docker workflow gene singularity vcf variants snv vep disease-gene-association indels annotation-tool vcfanno germline variant-annotations annotation-framework snvs
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Aug 11, 2026 - Python
🌳 Scalable ancestry from genomic data
genome ancestry snv genome-assembly genomic-data-analysis ancestrydna genomic-data ancestry-inference sequencing-data snv-call
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Sep 21, 2026 - Python
xGAP is an efficient, modular, extensible and fault-tolerant pipeline for massively parallelized genomic analysis/variant discovery from next-generation DNA sequencing data.
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Oct 21, 2020 - Python
Flexible Trio DNV detection on existing VCFs.
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Mar 4, 2026 - Python
Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)
github python vcf gatk variants snp annotator macaron snv annotation-framework snpeff snv-annotation codon snpcluster pcsnv
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May 18, 2020 - Python
A collection of software to work with genomic variants
vcf variants snv variant-filtration variant-analysis snvs trio de-novo-mutation single-nucleotide-variation de-novo-mutations compound-heterozygous um1da058230
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May 7, 2026 - Python
Genome assembly and variant benchmarks for Chinese Quartet
snv genome-assembly structural-variants indel chinese-quartet variant-benchmark haplotype-resolved-assembly
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Jun 20, 2024 - Python
Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).
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Sep 24, 2023 - Python
An adaptable method for analyzing SNVs, INDELs, and CNVs from Whole Exome Sequencing (WES) data, emphasizing germline variants.
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Feb 29, 2024 - Python
a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
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Aug 13, 2026 - Python
In this repository I backup the pipelines I write for the project I am involved
plots tas variant-calling wgs snv purity cnv wes dna-sequencing contamination-detection structural-variants vaf
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Jan 19, 2025 - Python
RAVA (Reference-based Analysis of Viral Alleles) is a Nextflow-based pipeline for non-longitudinal viral NGS data that generates interactive browser visualizations and aggregate mutation tables.
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Aug 18, 2026 - Python
Germline SNV calling and phasing from single cell sequencing (for macOS Sequoia and Rocky8).
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Sep 21, 2026 - Python
Dependency-free identification of branch-associated SNVs from rooted phylogenies and transposed NEXUS matrices.
python bioinformatics reproducible-research phylogenetics command-line-tool snv newick bacterial-genomics nexus-format
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Sep 1, 2026 - Python
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Nov 19, 2021 - Python
WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication
quality-control somatic-variants variant-calling maf snv purity cnv copy-number-variation variant-annotations
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Nov 20, 2023 - Python
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