A pipeline for scaffolding a genome assembly using Hi-C
☆13Nov 24, 2022Updated 3 years ago
Alternatives and similar repositories for hic-pipeline
Users that are interested in hic-pipeline are comparing it to the libraries listed below
Sorting:
- Add multiple thread function for genome comparison☆16Sep 29, 2021Updated 4 years ago
- Annotate Olfactory receptor CDS from genome☆10Apr 29, 2023Updated 2 years ago
- assembly evaluation tool☆35May 11, 2022Updated 3 years ago
- Ultra-efficient mapping-free structural variation genotyper☆20Jul 28, 2021Updated 4 years ago
- A Hi-C scaffolding method☆22Dec 22, 2021Updated 4 years ago
- use long sequenced reads to close gaps in assemblies☆41Sep 4, 2018Updated 7 years ago
- ☆13Nov 15, 2017Updated 8 years ago
- ☆10Jun 9, 2020Updated 5 years ago
- TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain☆21Jun 17, 2024Updated last year
- genotyping by Mapping-free ALternate-allele detection of known VAriants☆10Mar 6, 2023Updated 3 years ago
- The repository for codes developed to generated the Maize NC358 assemblies and analyses.☆10Apr 23, 2020Updated 5 years ago
- Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.☆24Dec 6, 2018Updated 7 years ago
- General analysis of HiC data, including compartment A/B, domains and loops.☆14Feb 17, 2023Updated 3 years ago
- A reliable gap filling pipeline for draft genomes☆11Sep 17, 2019Updated 6 years ago
- TreeBeST: Tree Building guided by Species Tree☆15Feb 17, 2011Updated 15 years ago
- We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a …☆32Jan 3, 2022Updated 4 years ago
- a fork of the gap-closing pipeline PBJelly☆15Jan 7, 2019Updated 7 years ago
- Set of script for the paper on the cattle graph genome☆13Jan 10, 2023Updated 3 years ago
- Code for building and testing variant ranking strategies☆17Aug 22, 2025Updated 6 months ago
- A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks☆18Sep 9, 2021Updated 4 years ago
- ☆15Aug 22, 2023Updated 2 years ago
- Software to assemble contigs/scaffolds into chromosomes using Hi-C data☆28Sep 26, 2024Updated last year
- A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly☆11Feb 28, 2017Updated 9 years ago
- parallelLastz: Running Lastz in parallel☆17Sep 13, 2024Updated last year
- Scripts used to perform analyses in Rice et al. (2023)☆16Dec 28, 2023Updated 2 years ago
- building a human pangenome from the HPRCy1v2 genbank accessioned assemblies☆15Feb 13, 2023Updated 3 years ago
- ☆14Mar 13, 2018Updated 7 years ago
- Nextflow pipeline for scaffolding genome assemblies with Hi-C reads☆16Nov 5, 2025Updated 4 months ago
- Whole Genome Annotation Pipeline☆16Jun 20, 2025Updated 8 months ago
- ☆15Aug 6, 2018Updated 7 years ago
- Tools for working with agp files☆19Jun 26, 2025Updated 8 months ago
- Derives consensus sequences from a set of long noisy reads by clustering and error correction.☆16Jul 20, 2021Updated 4 years ago
- Fast and frugal disk based k-mer counter☆14Apr 1, 2021Updated 4 years ago
- A machine learning-based genotyping tool for structural variation in short reads☆26Sep 15, 2025Updated 5 months ago
- Simple tools for working with Hi-C data☆18Dec 19, 2018Updated 7 years ago
- Detection and genotyping of structural variants☆20Oct 17, 2025Updated 4 months ago
- BUSCOMP: BUSCO Compiler and Comparison tool☆21Sep 19, 2024Updated last year
- The MafFilter genome alignment processor☆19Jan 6, 2026Updated 2 months ago
- MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads☆111Oct 2, 2020Updated 5 years ago