tseemann / kounta
🧮 🔢 Generate multi-sample k-mer count matrix from WGS
☆12Updated 5 years ago
Alternatives and similar repositories for kounta:
Users that are interested in kounta are comparing it to the libraries listed below
- ☆19Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 6 months ago
- Scaffolding with assembly likelihood optimization☆22Updated 4 years ago
- transposable element typing pipeline☆17Updated last year
- Annotated Genome Optimization Using Transcriptome Information☆19Updated 4 years ago
- genomic alignment similarity search tool☆18Updated 10 months ago
- Scaffolding with Ultralong Reads☆15Updated 4 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated last year
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆11Updated 4 months ago
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆24Updated 5 years ago
- Colinear block visualisation tool☆30Updated last year
- software to identify primers that can distinguish genomes☆21Updated 3 months ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Rapid discovery of reciprocal best blast pairs.☆10Updated 5 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆12Updated last year
- Location of structural errors in a genome assembly and structural variations between a pair of genomes☆11Updated 5 years ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Read contamination removal☆25Updated last year
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆17Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- Scripts to split reference and run mummer in parallel on an SGE cluster☆11Updated 8 years ago
- Haploidy and Size Completeness Estimation☆13Updated last year
- Disty McMatrixface - compute a distance matrix from a core genome alignment file☆14Updated 2 years ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- Extracts subgraphs or components from a graph in GFA format☆23Updated 5 months ago
- Quantifying the significance of genetic variation using probabilistic profile-based methods.☆19Updated 4 years ago
- ☆14Updated 3 years ago