Repository for code to produce phased 1000 Genomes Project haplotypes called against the CHM13v2 T2T reference genome.
☆15Jan 31, 2026Updated last month
Alternatives and similar repositories for phasing_T2T
Users that are interested in phasing_T2T are comparing it to the libraries listed below
Sorting:
- Targeted genotyper for complex polymorphic genes☆36Feb 27, 2026Updated last week
- An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes☆46Sep 22, 2025Updated 5 months ago
- A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data☆17Aug 30, 2025Updated 6 months ago
- Genotyping of copy number sensitive allele-specific haplotypes☆27Nov 6, 2025Updated 4 months ago
- Characterization of Structural Variation in Chinese samples☆18Dec 22, 2021Updated 4 years ago
- WDL’s and Dockerfiles for assembly QC process☆72Jul 26, 2025Updated 7 months ago
- Kmer based genotyper for short reads.☆23Oct 19, 2021Updated 4 years ago
- Accurate Typing of Diverse Immune-Related Gene Families from Long-Read Sequencing Data. It can handle HLA, KIR, IG, TCR, CYP gene familie…☆33Feb 19, 2026Updated 2 weeks ago
- ☆49Sep 4, 2025Updated 6 months ago
- ☆101Apr 22, 2024Updated last year
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆29Sep 21, 2024Updated last year
- ☆38Jan 14, 2026Updated last month
- Draw a dot plot from a paf alignment☆38Sep 18, 2025Updated 5 months ago
- Scripts and utilities for analyzing tandem repeats (TRs).☆42Feb 11, 2026Updated 3 weeks ago
- T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.☆98Dec 21, 2025Updated 2 months ago
- Genome-wide TR catalog and variation clusters described in [Weisburd, Dolzhenko, et al. 2024]☆17Feb 19, 2026Updated 2 weeks ago
- This repository contains the code developed for the NanOlympicsMod project.☆12Jan 29, 2024Updated 2 years ago
- Easy genomic regions for short-read variant calling☆45Sep 10, 2025Updated 5 months ago
- Kmer Analysis of Pileups for Genotyping☆36Jan 30, 2026Updated last month
- ☆44Feb 23, 2026Updated last week
- a lexicographically-based GTF/GFF sorter☆38Apr 27, 2025Updated 10 months ago
- Pangenome-based genome inference☆156Dec 1, 2025Updated 3 months ago
- an interactive visualization and interpretation framework of reference-projected pangenome graphs☆38Feb 15, 2025Updated last year
- ☆12Nov 26, 2025Updated 3 months ago
- scRNA-seq analysis beyond gene annotations using transcriptionally active regions (TARs) generated from sequence alignment data☆10Jul 25, 2022Updated 3 years ago
- Python-based web scraper for extracting gene summaries from GeneCards.☆11Oct 3, 2024Updated last year
- Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).☆104Jul 23, 2024Updated last year
- Code used to process and analyze structural variants and short tandem repeat variants profiled in 719 deeply sequenced whole genomes as p…☆11Jun 25, 2019Updated 6 years ago
- Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read.☆19Sep 23, 2025Updated 5 months ago
- ☆12Feb 16, 2026Updated 2 weeks ago
- https://molecular-neurogenetics.github.io/truster/☆11Jul 14, 2025Updated 7 months ago
- ☆13Feb 5, 2026Updated last month
- ☆10Nov 9, 2022Updated 3 years ago
- genomic variant frequency estimation☆11Sep 7, 2025Updated 5 months ago
- Probabilistic single-individual haplotyping☆10Mar 15, 2019Updated 6 years ago
- multi_tbx: a simple tool for indexing VCF files and extract variant records for variant data stored in multiple VCF files.☆10Jan 7, 2022Updated 4 years ago
- SOAP-HLA is a flow of sequencing data analysis pipeline to type all of the HLA genes in IMGT/HLA database using capture sequenced data or…☆10Jun 3, 2020Updated 5 years ago
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated 4 months ago
- A fast, scalable, and accurate local ancestry method.☆108Feb 11, 2026Updated 3 weeks ago