Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
☆17Sep 4, 2024Updated last year
Alternatives and similar repositories for Genome-on-Diet
Users that are interested in Genome-on-Diet are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- CLI to automate Nextflow pipeline testing☆12Dec 15, 2025Updated 6 months ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆42Apr 30, 2025Updated last year
- AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shar…☆28May 23, 2024Updated 2 years ago
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆18Jun 3, 2019Updated 7 years ago
- Analysis and visualization of RNA-Seq results☆32May 1, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- For when you just need a coverage plot.☆11Mar 26, 2021Updated 5 years ago
- GateKeeper: Fast Alignment Filter for DNA Short Read Mapping☆21Mar 5, 2019Updated 7 years ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Jun 23, 2023Updated 2 years ago
- This repository contains data and other materials related to the DeepPT manuscript☆18Mar 12, 2024Updated 2 years ago
- ☆12Feb 14, 2023Updated 3 years ago
- SparsePainter: fast, accurate and fine-scale chromosome painting software based on PBWT and HashMap☆19Feb 11, 2026Updated 4 months ago
- Metalign: efficient alignment-based metagenomic profiling via containment min hash☆32Sep 12, 2023Updated 2 years ago
- SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU arch…☆56Mar 31, 2023Updated 3 years ago
- Improved version of the Oxford Bioinformatics paper template☆25Feb 4, 2026Updated 4 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A Hi…☆31Dec 19, 2022Updated 3 years ago
- Nanopore direct RNA basecaller☆11Oct 27, 2022Updated 3 years ago
- Learning meaningful representations of genes☆21Jul 7, 2025Updated 11 months ago
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- VCF Observer is a VCF file analysis, comparison, and visualization tool.☆22Jan 3, 2025Updated last year
- Real-time analysis pipeline for nanopore 16S rRNA data☆15Nov 29, 2022Updated 3 years ago
- Map genetic variants and protein positions to protein interfaces in 3D☆13Sep 22, 2023Updated 2 years ago
- Integrate Any Omics: Towards genome-wide data integration for patient stratification☆61May 19, 2025Updated last year
- GWAS Survival Package in R☆13Jun 12, 2026Updated last week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- probability of mendelian error in trios.☆11Jan 27, 2016Updated 10 years ago
- Westlake BioBank for Chinese pilot project☆10May 17, 2023Updated 3 years ago
- An efficient tool for cross-population fixation index estimation on variant call format files☆11Mar 1, 2026Updated 3 months ago
- A Nextflow workflow for HLA typing using HLA-HD☆15Jul 3, 2024Updated last year
- Viral genome coverage evaluation for metagenomic diagnostics☆27Aug 19, 2025Updated 10 months ago
- HaploSweep is a method for detecting and categorizing soft and hard selective sweeps based on haplotype structure.☆11Sep 24, 2024Updated last year
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- Targeted genotyper for complex polymorphic genes☆42Updated this week
- Software for ancestry estimation in unrelated individuals☆25Jan 31, 2026Updated 4 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆15Apr 19, 2018Updated 8 years ago
- Julia package for the Napari multi-dimensional image viewer☆11Jun 21, 2022Updated 3 years ago
- Released code for the paper 'End-to-end Multiple Instance Learning for Whole-Slide Cytopathology of Urothelial Carcinoma'☆10Nov 24, 2021Updated 4 years ago
- Statistical inference of recent positive selection using IBD segments☆14Apr 20, 2026Updated last month
- Tandem repeat genotyping with long reads☆38Sep 23, 2025Updated 8 months ago
- Interacting Active Surfaces☆10Jul 12, 2022Updated 3 years ago
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆139Jun 12, 2026Updated last week