A filter algorithm with program to filter an alignment or mapping file
☆12May 15, 2025Updated 9 months ago
Alternatives and similar repositories for RAfilter
Users that are interested in RAfilter are comparing it to the libraries listed below
Sorting:
- ☆16Apr 3, 2023Updated 2 years ago
- a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).☆21Dec 5, 2023Updated 2 years ago
- T2Tools is a toolset contains several tools for T2T assembly, and it is under development.☆15Sep 17, 2025Updated 5 months ago
- ☆32Jan 3, 2025Updated last year
- Robust Eukaryotic Annotation Toolkit☆17Feb 28, 2025Updated last year
- De novo chromosome-level scaffolding and phasing tool using Hi-C☆30Nov 23, 2025Updated 3 months ago
- SRY: an effective method for sorting long-read of sex-limited (Y or W) chromosome.☆19Aug 1, 2023Updated 2 years ago
- Draw a dot plot from a paf alignment☆38Sep 18, 2025Updated 5 months ago
- Haplotype aware de novo assembly of diploid genome from long reads☆54Mar 16, 2022Updated 3 years ago
- An effective alignment tool for long noisy 3C data (e.g. Pore-C and C-walk)☆14Oct 23, 2024Updated last year
- Some components that speed up and reduce resource cost for original ALLHiC☆14Jun 21, 2025Updated 8 months ago
- C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on 3C-based data (Pore-C, CiFi, Hi-C，Omni-C).☆90Jan 25, 2026Updated last month
- Code repository for the T2T-Y paper☆24Jul 11, 2023Updated 2 years ago
- ☆27Aug 29, 2025Updated 6 months ago
- SV calling for diploid assemblies☆31Mar 22, 2024Updated last year
- ☆38Oct 6, 2025Updated 4 months ago
- ☆41May 19, 2025Updated 9 months ago
- Genome alignment and synteny plots☆33Jun 5, 2023Updated 2 years ago
- Scripts used to perform analyses in Rice et al. (2023)☆16Dec 28, 2023Updated 2 years ago
- Very simple and configurable all-in-one dotplot program☆14Apr 1, 2023Updated 2 years ago
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆69May 22, 2021Updated 4 years ago
- Tools for working with agp files☆19Jun 26, 2025Updated 8 months ago
- Nextflow pipeline for scaffolding genome assemblies with Hi-C reads☆16Nov 5, 2025Updated 4 months ago
- Repeat-aware polishing genomes assembled using HiFi long reads☆98Nov 12, 2025Updated 3 months ago
- Evaluate variant calls and its combination with k-mer multiplicity☆67Dec 2, 2022Updated 3 years ago
- ☆31Apr 7, 2025Updated 10 months ago
- Transfer HiFi read mappings from their own assembly contigs to a standard reference☆36Dec 30, 2025Updated 2 months ago
- ☆16Apr 9, 2021Updated 4 years ago
- ☆16Dec 25, 2024Updated last year
- Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement☆79Dec 3, 2025Updated 3 months ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆35Apr 23, 2025Updated 10 months ago
- test repository☆29Jul 6, 2023Updated 2 years ago
- An ultra-fast gzip file tools☆27Apr 25, 2024Updated last year
- Simple tools for working with Hi-C data☆18Dec 19, 2018Updated 7 years ago
- ☆18Jan 29, 2025Updated last year
- Application of pan-genome for population☆116Oct 26, 2025Updated 4 months ago
- A tool for performing collinearity-incorporating homology inference☆33Oct 7, 2023Updated 2 years ago
- A Rust library for storing generic genomic data by sorted chromosome name☆17Sep 26, 2024Updated last year