USDA-ARS-GBRU / PanPipesLinks
Test sets and pipeline scripts for pan-genomic graph analysis
☆17Updated 6 months ago
Alternatives and similar repositories for PanPipes
Users that are interested in PanPipes are comparing it to the libraries listed below
Sorting:
- A tool for recovering synteny blocks from multiple alignment☆30Updated 3 years ago
- Scripts to split reference and run mummer in parallel on an SGE cluster☆11Updated 8 years ago
- ☆25Updated this week
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆38Updated 9 months ago
- Genome assembly soft-masking using Red (REpeat Detector)☆18Updated 6 years ago
- Ploidy agnostic phasing pipeline and algorithm☆46Updated last year
- Prefix-renaming FASTA records really fast.☆17Updated last year
- Extracts subgraphs or components from a graph in GFA format☆23Updated 8 months ago
- ☆20Updated this week
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆27Updated 10 months ago
- use variant nesting information to flter overlapping sites from vg deconstruct output☆26Updated 2 months ago
- convert PAF format to CHAIN format☆32Updated 2 months ago
- Reference bias measuring toolkit☆18Updated 3 months ago
- Improved Phased Assembler☆28Updated 3 years ago
- A Rust implementation of sliding window stats over fastas.☆15Updated 2 years ago
- Phasing reads with secondary alignments☆19Updated 8 months ago
- Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.☆24Updated 6 years ago
- A Hi-C scaffolding method☆23Updated 3 years ago
- A comparative genome scaffolding tool☆17Updated 6 years ago
- Unzip assembly graphs with Hi-C data and/or long reads.☆28Updated 10 months ago
- PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers☆18Updated 2 months ago
- Convert RepeatMasker ".out" file into a gff3 with colors!!!☆21Updated 4 years ago
- base-level dotplots from PAF alignments☆26Updated 2 weeks ago
- SV genotyper for long reads with a variation graph☆12Updated 4 months ago
- Scaffolding with assembly likelihood optimization☆22Updated 4 years ago
- WinPCA. A package for windowed principal component analysis.☆30Updated 3 weeks ago
- ☆21Updated 2 weeks ago
- scripts to parse and analyse MCScanX collinearity output☆32Updated 5 years ago
- Tools for haplotype-wise reconstruction of pseudomolecules☆20Updated 10 months ago
- an interactive visualization and interpretation framework of reference-projected pangenome graphs☆37Updated 5 months ago