tongzhouxu / mashpitLinks
Sketch-based surveillance platform
☆13Updated last year
Alternatives and similar repositories for mashpit
Users that are interested in mashpit are comparing it to the libraries listed below
Sorting:
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Updated this week
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated 3 months ago
- Genome size estimation from long read overlaps☆79Updated 3 weeks ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- A long read simulator based on badread idea☆22Updated 3 years ago
- A tool to detect acquired AMR genes directly from long read sequencing data.☆18Updated 4 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆43Updated 2 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆33Updated last week
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Updated last year
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆18Updated 2 years ago
- Differential k-mer analysis☆39Updated last year
- GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.☆36Updated 6 months ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Updated last year
- Visualize microbial evolution at the SNP level!☆15Updated 4 months ago
- Colinear block visualisation tool☆31Updated last year
- Remove human reads from a sequencing run☆46Updated last week
- Extracts subgraphs or components from a graph in GFA format☆24Updated last year
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆39Updated last year
- convert variation graph alignments to coverage maps over nodes☆26Updated 3 weeks ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆62Updated 8 months ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆27Updated 8 months ago
- Disty McMatrixface - compute a distance matrix from a core genome alignment file☆14Updated 2 years ago
- mGEMS Genomic epidemiology with mixed samples☆15Updated last year
- software to identify primers that can distinguish genomes☆20Updated this week
- MetagenOmic read Re-Assigner and abundance quantifier☆18Updated 10 months ago
- Library of sketching functions used by PopPUNK☆31Updated 8 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- Iterate over minimizers of a DNA sequence☆31Updated last year