tseemann / seeka
Get microbial sequence data easier and faster
☆28Updated 5 years ago
Alternatives and similar repositories for seeka:
Users that are interested in seeka are comparing it to the libraries listed below
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 10 months ago
- Colinear block visualisation tool☆30Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated last month
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- A script for comparing old vs new versions of genome annotations☆20Updated last year
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- TAXnomic Profile Aggregation and STAndardisation☆35Updated 3 months ago
- frame-shift correction for long-read (meta)genomics☆32Updated last year
- Predict MLST directly from uncorrected long reads☆26Updated 2 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 4 months ago
- Intra-species bacterial contamination detection☆25Updated last week
- Recombination-free trees☆57Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 7 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆36Updated this week
- Genome size estimation from long read overlaps☆48Updated 2 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆43Updated this week
- Bacterial taxonomy construction and evaluation in R☆13Updated last year
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Split Kmer Analysis☆63Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago