tseemann / kountaLinks
🧮 🔢 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
Sorting:
- Colinear block visualisation tool☆31Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 4 months ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 weeks ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated 2 months ago
- Falcon2Fastg is a tool for converting a FALCON assembly to FASTG format to visualize with Bandage☆13Updated 9 years ago
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- Disty McMatrixface - compute a distance matrix from a core genome alignment file☆14Updated 2 years ago
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆11Updated 11 months ago
- genomic alignment similarity search tool☆18Updated 6 months ago
- ☆30Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆56Updated 7 months ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 6 years ago
- Masks recombinant regions in an alignment based on ClonalFrameML output☆10Updated 7 years ago
- ☆14Updated 4 years ago
- Intra-species bacterial contamination detection☆25Updated 9 months ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆24Updated 5 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 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
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 8 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- transposable element typing pipeline☆19Updated last year
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Updated last year
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- Library of sketching functions used by PopPUNK☆31Updated 7 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- Read contamination removal☆25Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago