alshai / vcf2msa
convert a multi-sample VCF file to a multiple sequence alignment (C)
☆13Updated 5 years ago
Related projects ⓘ
Alternatives and complementary repositories for vcf2msa
- run-length BWT tools for genomic sequences☆18Updated 2 years ago
- Lift-over alignments from variant-aware references☆34Updated last year
- Code for assembly approach presented in "Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspri…☆14Updated 11 months ago
- the pangenome graph evaluator☆23Updated 3 years ago
- Scripts used to perform analyses in Rice et al. (2023)☆14Updated 10 months ago
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆25Updated last month
- Extracting paths from assembly graphs☆22Updated 6 months ago
- Programs implementing the trio-binning genome assembly method☆19Updated 11 months ago
- MONI: A Pangenomic Index for Finding MEMs☆37Updated last month
- Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.☆29Updated 6 years ago
- use variant nesting information to flter overlapping sites from vg deconstruct output☆23Updated 4 months ago
- Compare different genome alignment tools using a wide range of genomes with different complexities.☆13Updated last year
- recompute GFA link overlaps☆25Updated 2 years ago
- FastK based version of Merqury☆22Updated last week
- Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding☆19Updated 2 months ago
- ☆32Updated last year
- Extracts subgraphs or components from a graph in GFA format☆22Updated 5 months ago
- assembly evaluation tool☆34Updated 2 years ago
- Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.☆20Updated 2 years ago
- An algorithm for centromere assembly using long error-prone reads☆26Updated 3 years ago
- pangenome analyses for complete genomes of great apes (and gibbon)☆16Updated 3 weeks ago
- Scaffolding with assembly likelihood optimization☆20Updated 3 years ago
- ☆16Updated 6 years ago
- ☆18Updated 2 months ago
- Set of script for the paper on the cattle graph genome☆13Updated last year
- A Hi-C scaffolding method☆22Updated 2 years ago
- Very simple and configurable all-in-one dotplot program☆12Updated last year
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆24Updated 6 months ago
- ☆17Updated 2 weeks ago
- Identification of segmental duplications in the genome☆26Updated 2 years ago