ekg / gafpack
convert variation graph alignments to coverage maps over nodes
☆20Updated 3 months ago
Related projects: ⓘ
- Extracts subgraphs or components from a graph in GFA format☆21Updated 3 months ago
- recompute GFA link overlaps☆25Updated 2 years ago
- Pangenome Graph Variation Format (PGVF)☆18Updated 3 years ago
- ☆19Updated 2 years ago
- the pangenome graph evaluator☆22Updated 3 years ago
- Long read aligner for cyclic and acyclic pangenome graphs☆35Updated 9 months ago
- Prefix-renaming FASTA records really fast.☆13Updated 2 months ago
- Iterate k-min-mers from a DNA sequence in Rust☆13Updated 5 months ago
- pangenome analyses for complete genomes of great apes (and gibbon)☆17Updated last month
- Statistics and analysis for variation graphs☆30Updated last month
- Align subreads to ccs reads☆13Updated last year
- Extracting paths from assembly graphs☆19Updated 4 months ago
- convert CHAIN format to PAF format☆13Updated 4 months ago
- Long-read aligner to pangenome graphs☆25Updated 4 months ago
- ☆15Updated 4 years ago
- extract MSAs from genome variation graphs☆33Updated 4 years ago
- GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.☆33Updated 7 months ago
- use variant nesting information to flter overlapping sites from vg deconstruct output☆22Updated 2 months ago
- MEMO: MEM-based pangenome indexing for k-mer queries☆16Updated 3 months ago
- Differential k-mer analysis☆33Updated 7 months ago
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆22Updated 10 months ago
- ☆16Updated 3 years ago
- VACmap: a long-read aligner specifically designed for complex structural variation discovery☆18Updated last week
- Pipeline to evaluate pangenomes, e.g. from the variation it contains or how well reads map☆10Updated 2 years ago
- Lightweight mosaic/somatic SV caller for long reads (WIP)☆26Updated 3 months ago
- Very simple and configurable all-in-one dotplot program☆12Updated last year
- Kmer based genotyper for short reads.☆23Updated 2 years ago
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆19Updated last month
- a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).☆19Updated 9 months ago
- Generate interactive dotplot from mummer4 output using plotly☆25Updated 4 years ago