VGP repository for the genome assembly working group
☆194Mar 31, 2026Updated 5 months ago
Alternatives and similar repositories for vgp-assembly
Users that are interested in vgp-assembly are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- k-mer based assembly evaluation☆355Jul 6, 2026Updated 2 months ago
- The Vertebrate Genomes Project Mitogenome Assembly Pipeline☆19Mar 26, 2023Updated 3 years ago
- Evaluate variant calls and its combination with k-mer multiplicity☆73Dec 2, 2022Updated 3 years ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆189May 17, 2024Updated 2 years ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆576Feb 14, 2024Updated 2 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.
- haplotypic duplication identification tool☆295Oct 30, 2025Updated 10 months ago
- A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulatio…☆131Jun 18, 2026Updated 3 months ago
- Find, circularise and annotate mitogenome from PacBio assemblies☆201May 11, 2025Updated last year
- Scaffolding with Ultralong Reads☆15Nov 11, 2020Updated 5 years ago
- Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).☆118Jul 23, 2024Updated 2 years ago
- Simple tools for working with Hi-C data☆20Dec 19, 2018Updated 7 years ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆180Oct 20, 2024Updated last year
- Evaluation and polishing workflows for T2T genome assemblies☆168Sep 15, 2026Updated last week
- Fast and accurately polish the genome generated by long reads.☆246Jan 9, 2025Updated last year
- 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.
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆467Jun 17, 2026Updated 3 months ago
- Yet another Hi-C scaffolding tool☆183Nov 4, 2024Updated last year
- FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds☆72Nov 12, 2020Updated 5 years ago
- assembly evaluation tool☆35May 11, 2022Updated 4 years ago
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆588Sep 7, 2026Updated 2 weeks ago
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆173May 30, 2021Updated 5 years ago
- scripts for the project of seven thaliana genomes assembly☆42May 22, 2021Updated 5 years ago
- Generate an interactive dot plot from mummer or minimap alignments☆220Jan 17, 2024Updated 2 years ago
- Yet another k-mer analyzer☆177Dec 30, 2025Updated 8 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- 3D de novo assembly (3D DNA) pipeline☆229Nov 29, 2023Updated 2 years ago
- Tools for manipulating sequence graphs in the GFA and rGFA formats☆253Dec 16, 2025Updated 9 months ago
- software tools for haplotype assembly from sequence data☆233Feb 9, 2025Updated last year
- Fast genome analysis from unassembled short reads☆327Apr 8, 2024Updated 2 years ago
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆419Aug 25, 2026Updated 3 weeks ago
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆149Apr 13, 2026Updated 5 months ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆119Jun 6, 2021Updated 5 years ago
- Close assembly gaps using long-reads at high accuracy.☆52Feb 20, 2024Updated 2 years ago
- An accurate GFF3/GTF lift over pipeline☆557Aug 1, 2023Updated 3 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A program for assessing the T2T genome continuity and completeness☆97Sep 8, 2026Updated 2 weeks ago
- the pangenome graph builder☆515Jul 24, 2026Updated last month
- A genomic k-mer counter (and sequence utility) with nice features.☆190Jul 21, 2026Updated 2 months ago
- Reduction of Althaps and Duplicate Contigs for Improved Downstream Analysis☆21Jun 28, 2026Updated 2 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆250Sep 6, 2024Updated 2 years ago
- Mapping pipeline for data generated using Arima-HiC☆85May 22, 2024Updated 2 years ago
- ☆78Jun 12, 2020Updated 6 years ago