De novo genome assembly and multisample variant calling
☆113Mar 28, 2019Updated 7 years ago
Alternatives and similar repositories for mccortex
Users that are interested in mccortex are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Genome inference from a population reference graph☆96Apr 1, 2025Updated last year
- reference free variant assembly☆34Jul 14, 2023Updated 2 years ago
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆124Aug 24, 2023Updated 2 years ago
- Classify sequencing reads using MinHash.☆48Apr 6, 2020Updated 6 years ago
- A genomic minhashing implementation in Rust☆103Jun 17, 2025Updated 11 months 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.
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Nov 27, 2025Updated 6 months ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆53Mar 12, 2024Updated 2 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated 2 years ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆55May 17, 2022Updated 4 years ago
- Chromosome-level scaffolding using multiple references☆167Sep 8, 2024Updated last year
- d'accord is a non hybrid long read consensus program based on local de Bruijn graph assembly☆19Sep 12, 2018Updated 7 years ago
- Population-scale genotyping using pangenome graphs☆199Jan 9, 2025Updated last year
- High-performance error correction for Illumina resequencing data☆74May 31, 2016Updated 10 years ago
- Fast and memory-efficient sequencing error corrector☆94Jan 4, 2026Updated 5 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Jan 18, 2019Updated 7 years ago
- GAPPadder is tool for closing gaps on draft genomes with short sequencing data☆28Jun 1, 2017Updated 9 years ago
- alignment to variation graph inducer☆159Apr 11, 2026Updated last month
- A method for variant graph genotyping based on exact alignment of k-mers☆87Apr 1, 2019Updated 7 years ago
- StriDe Assembler☆25Nov 23, 2017Updated 8 years ago
- Reference-free variant discovery in large eukaryotic genomes☆42Jul 13, 2021Updated 4 years ago
- Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs☆224Oct 23, 2025Updated 7 months ago
- Histosketching Using Little Kmers☆57May 25, 2023Updated 3 years ago
- Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters☆23Apr 1, 2019Updated 7 years 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.
- [IMPORTANT: not for real data analysis, only for algorithm evaluation] fast and accurate alignment tool for PacBio and Nanopore long read…☆125Sep 10, 2018Updated 7 years ago
- SKESA assembler☆126Oct 11, 2024Updated last year
- Population Reference Graphs for the HLA and MHC.☆35Dec 18, 2018Updated 7 years ago
- Squeakr: An Exact and Approximate k -mer Counting System☆86Feb 23, 2025Updated last year
- Location of structural errors in a genome assembly and structural variations between a pair of genomes☆11Sep 27, 2019Updated 6 years ago
- Pan-genome inference and genotyping with long noisy or short accurate reads☆118Dec 13, 2024Updated last year
- De novo assembly based variant calling pipeline for Illumina short reads☆110Nov 30, 2020Updated 5 years ago
- Code examples of fast and simple k-mer counters for tutorial purposes☆172Mar 10, 2020Updated 6 years ago
- Fast and accurate genomic distances using HyperLogLog☆162Jan 19, 2023Updated 3 years ago
- 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.
- Recombination-free trees☆70Apr 26, 2026Updated last month
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆354Jul 19, 2025Updated 10 months ago
- deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph☆31Jan 19, 2021Updated 5 years ago
- SaffronTree: Reference free rapid phylogenetic tree construction from raw read data☆25Jun 11, 2020Updated 5 years ago
- De novo genome assembler.☆12Jul 30, 2018Updated 7 years ago
- Scaffolding with assembly likelihood optimization☆21Dec 14, 2020Updated 5 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆112Mar 11, 2026Updated 2 months ago