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).
☆18Sep 4, 2024Updated 2 years ago
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☆13Dec 15, 2025Updated 9 months ago
- 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…☆19Jun 3, 2019Updated 7 years ago
- AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.or…☆24Apr 12, 2023Updated 3 years ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆42Apr 30, 2025Updated last year
- 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.
- Analysis and visualization of RNA-Seq results☆34Aug 25, 2026Updated last month
- For when you just need a coverage plot.☆11Mar 26, 2021Updated 5 years ago
- GateKeeper: Fast Alignment Filter for DNA Short Read Mapping☆23Mar 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 3 years ago
- This repository contains data and other materials related to the DeepPT manuscript☆17Mar 12, 2024Updated 2 years ago
- Metalign: efficient alignment-based metagenomic profiling via containment min hash☆32Sep 12, 2023Updated 3 years ago
- ☆12Feb 14, 2023Updated 3 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…☆57Mar 31, 2023Updated 3 years ago
- Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A Hi…☆32Dec 19, 2022Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Nanopore direct RNA basecaller☆11Oct 27, 2022Updated 3 years ago
- Real-time analysis pipeline for nanopore 16S rRNA data☆15Nov 29, 2022Updated 3 years ago
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- A nextflow pipeline for calling modifications in nanopore reads.☆17Updated this week
- fastrgz is a fast and efficient gzip compression tool for sequencing data (FASTQ)☆31Jun 18, 2026Updated 3 months ago
- Map genetic variants and protein positions to protein interfaces in 3D☆13Sep 22, 2023Updated 3 years ago
- GWAS Survival Package in R☆13Jun 12, 2026Updated 3 months ago
- Integrate Any Omics: Towards genome-wide data integration for patient stratification☆62May 19, 2025Updated last year
- probability of mendelian error in trios.☆11Jan 27, 2016Updated 10 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- ☆15May 22, 2025Updated last year
- An efficient tool for cross-population fixation index estimation on variant call format files☆11Mar 1, 2026Updated 6 months ago
- Westlake BioBank for Chinese pilot project☆10May 17, 2023Updated 3 years ago
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- ☆18May 14, 2025Updated last year
- Learning meaningful representations of genes☆21Jul 7, 2025Updated last year
- ☆20Jan 23, 2026Updated 8 months ago
- Genotyping of paralog specific gene types☆22Aug 28, 2026Updated 3 weeks ago
- HaploSweep is a method for detecting and categorizing soft and hard selective sweeps based on haplotype structure.☆11Sep 24, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- SparsePainter: fast, accurate and fine-scale chromosome painting software based on PBWT and HashMap☆19Updated this week
- VCF Observer is a VCF file analysis, comparison, and visualization tool.☆23Jan 3, 2025Updated last year
- ☆15Apr 19, 2018Updated 8 years ago
- Julia package for the Napari multi-dimensional image viewer☆11Jun 21, 2022Updated 4 years ago
- Statistical inference of recent positive selection using IBD segments☆14Apr 20, 2026Updated 5 months ago
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆148Sep 17, 2026Updated last week
- First place algorithm in ISBI 2024 Light My Cell competition, label-free cell painting☆14Jun 3, 2024Updated 2 years ago