A fast and memory-efficient k-mer counter with GPU-support
☆38Oct 26, 2020Updated 5 years ago
Alternatives and similar repositories for gerbil
Users that are interested in gerbil are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- De novo genome assembler.☆11Jul 30, 2018Updated 7 years ago
- Squeakr: An Exact and Approximate k -mer Counting System☆86Feb 23, 2025Updated last year
- k-mer similarity analysis pipeline☆22Nov 20, 2025Updated 4 months ago
- PySeqArray: data manipulation of whole-genome sequencing variants with SeqArray files in Python (pre-release version)☆14Aug 25, 2017Updated 8 years ago
- Non-parametric structural variant genotyper☆15Nov 18, 2021Updated 4 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Fast and frugal disk based k-mer counter☆327Mar 10, 2026Updated 3 weeks ago
- Fast and accurate set similarity estimation via containment min hash☆42Jul 19, 2024Updated last year
- A collection of CSV/TSV Utilities☆13Jun 2, 2020Updated 5 years ago
- Streaming algorithm for computing kmer statistics for massive genomics datasets☆54Feb 18, 2020Updated 6 years ago
- Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, et…☆97May 20, 2025Updated 10 months ago
- Lossless VCF compression☆21Mar 4, 2022Updated 4 years ago
- Toolkit for extracting SVs from long sequences and benchmarking variant callers☆13Jan 10, 2017Updated 9 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- Polygenic score calculation from VCF in Nim.☆15Nov 22, 2020Updated 5 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Bonsai: Fast, flexible taxonomic analysis and classification☆70Apr 9, 2024Updated 2 years ago
- This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye R…☆18May 21, 2017Updated 8 years ago
- k-mer counting software☆40Feb 8, 2022Updated 4 years ago
- Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long read…☆12Jan 22, 2020Updated 6 years ago
- Histosketching Using Little Kmers☆57May 25, 2023Updated 2 years ago
- interactive Multi Objective K-mer Analysis☆24Mar 5, 2023Updated 3 years ago
- Sample Contamination Estimate from VCF☆20Nov 6, 2024Updated last year
- A fast multi-threaded k-mer counter☆532Mar 20, 2024Updated 2 years ago
- IndexTools is a toolkit for extremely fast NGS analysis based on index files.☆17Aug 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.
- Utilities to detect and profile `het-kmers`☆12Aug 5, 2024Updated last year
- ☆12Apr 8, 2021Updated 5 years ago
- An experimental tool to find approximate max-cuts in a large graph☆10Apr 28, 2021Updated 4 years ago
- Alignment algorithm for short Illumina reads to a de Bruijn graph☆17Jun 4, 2019Updated 6 years ago
- Copy number estimation of highly duplicated sequences☆10Aug 15, 2017Updated 8 years ago
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆198Mar 8, 2022Updated 4 years ago
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆21Oct 20, 2023Updated 2 years ago
- Fast and accurate genomic distances using HyperLogLog☆163Jan 19, 2023Updated 3 years ago
- DartMinHash: Fast Sketching for Weighted Sets☆12Dec 8, 2025Updated 4 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- Parallel implementation of the LAST aligner☆18Nov 27, 2016Updated 9 years ago
- Index and query k-mer matrices in BGZF☆12Apr 30, 2018Updated 7 years ago
- Numerical Encoding for Human Genetic Variants☆42Jun 8, 2023Updated 2 years ago
- Aligns short reads using dynamic seed size with strobemers☆194Apr 1, 2026Updated last week
- CUDASW++4.0: Ultra-fast GPU-based Smith-Waterman Protein Sequence Database Search☆46Dec 10, 2025Updated 3 months ago
- A Python package for fast operations on 1-dimensional genomic signal tracks☆23Apr 3, 2020Updated 6 years ago
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Nov 27, 2025Updated 4 months ago