OmarOakheart / nPhaseView external linksLinks
Ploidy agnostic phasing pipeline and algorithm
☆49Jan 3, 2024Updated 2 years ago
Alternatives and similar repositories for nPhase
Users that are interested in nPhase are comparing it to the libraries listed below
Sorting:
- The MafFilter genome alignment processor☆19Jan 6, 2026Updated last month
- reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graph☆18Jul 26, 2023Updated 2 years ago
- flopp is a software package for single individual haplotype phasing of polyploid organisms from long read sequencing.☆37Nov 3, 2023Updated 2 years ago
- Highly customizable, ambiguity-aware dotplots for visual sequence analyses☆107Updated this week
- Gapless provides combined scaffolding, gap-closing and assembly correction with long reads☆38Mar 5, 2023Updated 2 years ago
- A Hi-C scaffolding method☆22Dec 22, 2021Updated 4 years ago
- SV calling for diploid assemblies☆31Mar 22, 2024Updated last year
- C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.☆87Jan 25, 2026Updated 2 weeks ago
- Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding☆20Mar 3, 2025Updated 11 months ago
- De novo chromosome-level scaffolding and phasing tool using Hi-C☆29Nov 23, 2025Updated 2 months ago
- Filter of Pairwise Alignement☆44Jan 31, 2022Updated 4 years ago
- A program for assessing the T2T genome continuity☆92Dec 14, 2025Updated 2 months ago
- Yet another k-mer analyzer☆158Dec 30, 2025Updated last month
- Genome mapping and spliced alignment of cDNA or amino acid sequences☆110Jan 26, 2026Updated 2 weeks ago
- A genome assembly assessment pipeline.☆37Nov 20, 2023Updated 2 years ago
- ☆41May 19, 2025Updated 8 months ago
- Repeat-aware polishing genomes assembled using HiFi long reads☆98Nov 12, 2025Updated 3 months ago
- Unzip assembly graphs with Hi-C data and/or long reads.☆27Sep 20, 2024Updated last year
- ☆49Nov 24, 2025Updated 2 months ago
- Haplotype aware de novo assembly of diploid genome from long reads☆54Mar 16, 2022Updated 3 years ago
- Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to s…☆109Jan 30, 2026Updated 2 weeks ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆105Jun 6, 2021Updated 4 years ago
- Tool for globally phasing diploid assembly graphs with orthogonal data☆43Nov 25, 2024Updated last year
- A wrapper for calling small variants from human germline high-coverage single-sample Illumina data☆14Jul 21, 2019Updated 6 years ago
- A plant organellar Graphical Fragment Assembly toolkit☆16Sep 10, 2025Updated 5 months ago
- Collection of utilities for working with PacBio-based assemblies☆13Apr 2, 2023Updated 2 years ago
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated 10 months ago
- A toolkit for identifying recombination and recombinant genotypes☆26Dec 3, 2025Updated 2 months ago
- ☆78Jun 12, 2020Updated 5 years ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆35Apr 23, 2025Updated 9 months ago
- This is the standalone version of the EviAnn pipeline☆136Feb 5, 2026Updated last week
- Tree reconstruction of ancestry using incomplete lineage sorting☆11Jan 9, 2026Updated last month
- Annotation of cryptic transposon variants using Hidden Markov Models to detect conserved terminal features.☆10Jan 27, 2026Updated 2 weeks ago
- Fast and accurate coordinate conversion between assemblies☆118Oct 9, 2025Updated 4 months ago
- PSAURON is a machine learning model for rapid assessment of protein coding gene annotation☆53Dec 11, 2025Updated 2 months ago
- FastK based version of Merqury☆30Jan 19, 2026Updated 3 weeks ago
- Long-reads Gap-free Chromosome-scale Assembler☆79Mar 21, 2023Updated 2 years ago
- Validate and edit small eukaryotic genome assemblies☆32Apr 28, 2023Updated 2 years ago
- ☆33Aug 2, 2022Updated 3 years ago