andrewjpage / krocusLinks
Predict MLST directly from uncorrected long reads
☆27Updated 3 years ago
Alternatives and similar repositories for krocus
Users that are interested in krocus are comparing it to the libraries listed below
Sorting:
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 2 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆62Updated 3 months ago
- Recombination-free trees☆60Updated last month
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago
- Intra-species bacterial contamination detection☆25Updated 7 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated last week
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Colinear block visualisation tool☆31Updated last year
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 weeks ago
- Split Kmer Analysis☆65Updated 3 years ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Updated last year
- Extract subsets of ONT (Nanopore) reads based on time☆22Updated last year
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- ☆37Updated 3 years ago
- List and download schemes from pubMLST.org and other BIGSDB servers☆10Updated 11 months ago
- Whole genome core alignments from multiple draft genomes☆13Updated 9 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 5 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆26Updated 3 years ago
- Order and orientation of complete bacterial genomes☆28Updated 2 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆43Updated 6 months ago
- REcombination BARcode detector.☆16Updated last year
- Plasmid exploration of bacterial genomes☆18Updated 3 years ago
- Genome size estimation from long read overlaps☆61Updated 2 weeks ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago