mbhall88 / psdmLinks
Compute a pairwise SNP distance matrix from one or two alignment(s)
☆25Updated last year
Alternatives and similar repositories for psdm
Users that are interested in psdm are comparing it to the libraries listed below
Sorting:
- Visualize microbial evolution at the SNP level!☆15Updated 2 months ago
- Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs☆31Updated last week
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Updated 10 months ago
- Genome size estimation from long read overlaps☆61Updated 2 weeks ago
- HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NG…☆12Updated last year
- Fast and exact gap-affine partial order alignment☆54Updated 3 weeks ago
- k-mers and the like☆22Updated last week
- fast, multithreaded sourmash operations: search, compare, and gather.☆24Updated this week
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated 4 months ago
- Wavefront alignment algorithm (WFA) in Golang☆32Updated 2 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆43Updated 2 years ago
- Differential k-mer analysis☆37Updated last year
- software to identify primers that can distinguish genomes☆20Updated 8 months ago
- Sketch-based surveillance platform☆13Updated 9 months ago
- Variant call verification☆16Updated 5 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆26Updated last month
- Long read aligner for cyclic and acyclic pangenome graphs☆39Updated last year
- Extracts subgraphs or components from a graph in GFA format☆24Updated 10 months ago
- Manipulate and generate figures for trees in Newick format☆22Updated 2 months ago
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆21Updated last year
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆34Updated 10 months ago
- Sketch phylogenetic trees and networks☆23Updated last month
- Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 6 months ago
- Remove human reads from a sequencing run☆40Updated 2 months ago
- convert variation graph alignments to coverage maps over nodes☆24Updated 3 months ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Updated 10 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆32Updated last month
- GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.☆36Updated 4 months ago
- Basecalling configuration prediction through FASTQ files☆29Updated 4 months ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆43Updated last month