pangenome / maffer
extract MSAs from genome variation graphs
☆33Updated 4 years ago
Alternatives and similar repositories for maffer:
Users that are interested in maffer are comparing it to the libraries listed below
- GFA insert into GenomicSQLite☆48Updated 3 years ago
- the pangenome graph evaluator☆25Updated 3 years ago
- building a human pangenome from the HPRCy1v2 genbank accessioned assemblies☆14Updated 2 years ago
- recompute GFA link overlaps☆25Updated 2 years ago
- GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.☆36Updated 3 weeks ago
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆26Updated 5 months ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆34Updated last week
- Method to optimally select samples for validation and resequencing☆27Updated 3 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆24Updated 11 months ago
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆24Updated 4 years ago
- General purpose utility related to GAF files☆22Updated last month
- Convert HAL to VG☆21Updated 7 months ago
- convert variation graph alignments to coverage maps over nodes☆23Updated last month
- Haplotype-aware genome assembly toolkit☆29Updated 5 years ago
- This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files☆25Updated 2 months ago
- Minimizer-based assembly scaffolding and mapping using long reads☆37Updated 5 months ago
- Extracts subgraphs or components from a graph in GFA format☆23Updated 3 months ago
- Scaffolding with Ultralong Reads☆15Updated 4 years ago
- Assembler for raw de novo genome assembly of long uncorrected reads.☆37Updated 5 years ago
- Improved Phased Assembler☆28Updated 3 years ago
- ☆41Updated last month
- assembly evaluation tool☆34Updated 2 years ago
- Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence informa…☆44Updated last year
- ☆26Updated 3 years ago
- ☆17Updated 3 weeks ago
- Statistics and analysis for variation graphs☆38Updated 2 months ago
- A tool for the recovery of unassembled telomeres from soft-clipped read alignments.☆35Updated 2 months ago
- ☆28Updated last year
- Identification of segmental duplications in the genome☆26Updated 3 years ago
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆37Updated 4 months ago