genome-analysis
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[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
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Dec 14, 2024 - Shell
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
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Mar 5, 2025 - Python
Randomly subsample sequencing reads or alignments
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Nov 29, 2024 - Rust
Earl Grey: A fully automated TE curation and annotation pipeline
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Mar 25, 2025 - Python
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
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Oct 28, 2023 - Python
De novo genome assembly and multisample variant calling
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Mar 28, 2019 - C
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
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Mar 12, 2025 - Nextflow
Long-reads Gap-free Chromosome-scale Assembler
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Mar 21, 2023 - Python
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
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Oct 28, 2020 - Python
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
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Sep 14, 2024 - Python
RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al. (published athttps://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).
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Dec 9, 2024 - C
Bioinformatics on GCP, AWS or Azure
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Mar 8, 2025 - Shell
BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGABhttps://doi.org/10.1093/nargab/lqad004)
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May 10, 2023 - C
Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
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Dec 22, 2024 - Python
non-redundant, compressed, journalled, file-based storage for biological sequences
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Mar 19, 2025 - Python
An Efficient Swiss Army Knife for Population Genomic Analyses in R
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May 21, 2024 - R
visual analysis of your VCF files
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Dec 3, 2022 - R
Basic and fast GWAS functions for QQ and Manhattan plots (incl. gene names)
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Feb 8, 2024 - R
A minimal genetic data explorer that processes all genetic information locally.
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Nov 1, 2023 - JavaScript
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