USDA-ARS-GBRU / PanPipesLinks
Test sets and pipeline scripts for pan-genomic graph analysis
☆17Updated 5 months ago
Alternatives and similar repositories for PanPipes
Users that are interested in PanPipes are comparing it to the libraries listed below
Sorting:
- A Rust implementation of sliding window stats over fastas.☆15Updated 2 years ago
- Genome assembly soft-masking using Red (REpeat Detector)☆18Updated 6 years ago
- Ploidy agnostic phasing pipeline and algorithm☆46Updated last year
- A tool for recovering synteny blocks from multiple alignment☆30Updated 3 years ago
- Prefix-renaming FASTA records really fast.☆17Updated last year
- Scripts to split reference and run mummer in parallel on an SGE cluster☆11Updated 8 years ago
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆27Updated 9 months ago
- Phasing reads with secondary alignments☆19Updated 7 months ago
- Extracts subgraphs or components from a graph in GFA format☆23Updated 7 months ago
- Improved Phased Assembler☆28Updated 3 years ago
- ☆20Updated this week
- ☆24Updated 7 months ago
- SV genotyper for long reads with a variation graph☆12Updated 3 months ago
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆38Updated 9 months ago
- PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers☆18Updated last month
- an interactive visualization and interpretation framework of reference-projected pangenome graphs☆36Updated 5 months ago
- a python package for finding tandem repeats from genomic sequences☆28Updated 3 months ago
- Tool for decomposition centromeric assemblies and long reads into monomers☆36Updated 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…☆45Updated 2 years ago
- Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.☆24Updated 6 years ago
- use variant nesting information to flter overlapping sites from vg deconstruct output☆26Updated last month
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆35Updated 2 months ago
- Unzip assembly graphs with Hi-C data and/or long reads.☆28Updated 9 months ago
- Scaffolding with assembly likelihood optimization☆22Updated 4 years ago
- A comparative genome scaffolding tool☆17Updated 6 years ago
- Lightweight mosaic/somatic SV caller for long reads (WIP)☆29Updated 7 months ago
- Convert RepeatMasker ".out" file into a gff3 with colors!!!☆21Updated 4 years ago
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆24Updated 5 years ago
- ☆25Updated 10 months ago
- A viewer for multiple alignment format (MAF) files in JBrowse 2☆12Updated 3 weeks ago