Pipeline for genome scaffolding by modelling distributions of HiC pairs
☆11Dec 7, 2022Updated 3 years ago
Alternatives and similar repositories for scaffHiC
Users that are interested in scaffHiC are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.☆28Jun 18, 2026Updated last week
- This pipeline is used to distinguish allotetraploid subgenomes.☆11Apr 8, 2024Updated 2 years ago
- ☆10Jun 9, 2020Updated 6 years ago
- ☆16May 7, 2023Updated 3 years ago
- ☆13May 27, 2025Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- assembly evaluation tool☆35May 11, 2022Updated 4 years ago
- Some components that speed up and reduce resource cost for original ALLHiC☆15Jun 21, 2025Updated last year
- T2Tools is a toolset contains several tools for T2T assembly, and it is under development.☆17Sep 17, 2025Updated 9 months ago
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆69May 22, 2021Updated 5 years ago
- several scripts for bioinformatics☆25Nov 27, 2025Updated 7 months ago
- Command line tool to plot genomic coverage from a BAM file☆14Apr 5, 2023Updated 3 years ago
- ☆15Apr 16, 2026Updated 2 months ago
- ☆37Feb 22, 2023Updated 3 years ago
- A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, a…☆16Jan 25, 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.
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulatio…☆125Jun 18, 2026Updated last week
- Hybrid error correction approach for long reads using overlap graph☆11Sep 26, 2023Updated 2 years ago
- The tools are used for displaying hic signal of genome☆26Jan 4, 2021Updated 5 years ago
- i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.☆17Jun 28, 2024Updated 2 years ago
- ☆13Nov 15, 2017Updated 8 years ago
- ☆78Jun 12, 2020Updated 6 years ago
- The MafFilter genome alignment processor☆19Apr 10, 2026Updated 2 months ago
- Homologizer: phasing gene copies into polyploid subgenomes☆13Feb 3, 2026Updated 4 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Dynamic Elongation of a Genome Assembly Path☆25Apr 29, 2026Updated 2 months ago
- ☆26Apr 22, 2025Updated last year
- Tool for globally phasing diploid assembly graphs with orthogonal data☆43Nov 25, 2024Updated last year
- Gapless provides combined scaffolding, gap-closing and assembly correction with long reads☆39Mar 5, 2023Updated 3 years ago
- ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-orth…☆25Jan 21, 2026Updated 5 months ago
- Diamond2GO is a set of tools that can rapidly assign Gene Ontology (GO) terms and perform functional enrichment for large-scale functiona…☆26Mar 11, 2026Updated 3 months ago
- ☆15Jan 19, 2022Updated 4 years ago
- This is a method to find telomeres and centromeres in plants.☆43Jun 17, 2023Updated 3 years ago
- A Hi-C scaffolding method☆22Dec 22, 2021Updated 4 years ago
- 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.
- Annotation helper tool for the manual curation of transposable element consensus sequences☆55Mar 5, 2025Updated last year
- EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to a…☆26Mar 11, 2023Updated 3 years ago
- A legacy repository. Was replaced by distiller, cooler, and cooltools.☆21Mar 4, 2020Updated 6 years ago
- Genome alignment and synteny plots☆35Mar 24, 2026Updated 3 months ago
- Simple library/pipeline to generate and handle Hi-C data.☆42May 18, 2026Updated last month
- Hi-C Interaction Frequency Inference (HIFI): High-resolution estimation of DNA-DNA interaction frequency from Hi-C data☆24Sep 28, 2022Updated 3 years ago
- Pipelines for the production of Treeval data☆31Jun 18, 2026Updated last week