Genomic data manipulation tool
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Updated
Jun 6, 2024 - Python
Genomic data manipulation tool
Bioinformatics on GCP, AWS or Azure
Multiple sequence alignment tool that builds on the concept of seed-and-extend algorithms
non-redundant, compressed, journalled, file-based storage for biological sequences
OpenAPI-based REST interface to biological sequences and sequence metadata
provides common tools and lookup tables used primarily by the hgvs and uta packages
Genome assembly steps (Haliotis asinina)
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
This is a template for all assembly projects. Please read the instructions below on how to use it.
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
Library-free horizontal transfer detection, with a focus on transposable element invasions
Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
Earl Grey: A fully automated TE curation and annotation pipeline
Genomics workflows for CPG using Hail Batch
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
tairaccession python package for interaction with tair and analyzing arabidopsis genome.
RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)
An Efficient Swiss Army Knife for Population Genomic Analyses in R
The genome of the contractile demosponge Tethya wilhelma
Pipeline to identify repetitive elements on non-model species genomes.
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