ptrebert / project-diploid-assembly
Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data
☆16Updated last year
Alternatives and similar repositories for project-diploid-assembly:
Users that are interested in project-diploid-assembly are comparing it to the libraries listed below
- A module for improving the insertion sequences of structural variant calls☆30Updated 3 years ago
- Phase reads, assemble haplotypes and detect SVs☆19Updated 4 years ago
- Identification of segmental duplications in the genome☆27Updated 3 years ago
- building a human pangenome from the HPRCy1v2 genbank accessioned assemblies☆14Updated 2 years ago
- A long-read analysis toolbox for cancer and population genomics☆23Updated 2 months ago
- exploratory scripts for clustering ccs amplicon data☆10Updated 4 years ago
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆29Updated 7 months ago
- An algorithm for centromere assembly using long error-prone reads☆26Updated 3 years ago
- VCF files of SVs using long-read sequencing (LRS).☆22Updated 3 years ago
- Convert HAL to VG☆22Updated 8 months ago
- Method to optimally select samples for validation and resequencing☆27Updated 4 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆24Updated last year
- Exact Tandem Repeat Finder (not a TRF replacement)☆49Updated 5 years ago
- Kmer based genotyper for short reads.☆23Updated 3 years ago
- Tool for decomposition centromeric assemblies and long reads into monomers☆36Updated 2 years ago
- ☆14Updated last year
- Variant annotation and merging pipeline☆33Updated last month
- FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…☆26Updated 2 years ago
- Improved Phased Assembler☆28Updated 3 years ago
- A tool set to assess the quality of the per read phasing and reduce the errors.☆12Updated 4 years ago
- ☆34Updated 5 years ago
- Symmetric DUST for finding low-complexity regions in DNA sequences☆38Updated last year
- Population-wide Deletion Calling☆35Updated 2 weeks ago
- ☆16Updated 3 months ago
- Automation of pipelines that depend on preexisting assembly, polishing, and alignment tools. Performance evaluation and visualization of …☆14Updated 4 years ago
- SV genotyping with long reads☆40Updated last year
- use variant nesting information to flter overlapping sites from vg deconstruct output☆26Updated 10 months ago
- ☆21Updated 5 years ago
- ☆16Updated 3 years ago
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆24Updated 5 years ago