staphopia / staphopia-sccmec
Archived - please see updated sccmec tool at link below
☆13Updated 5 months ago
Alternatives and similar repositories for staphopia-sccmec:
Users that are interested in staphopia-sccmec are comparing it to the libraries listed below
- CFSAN Shigella Typing Pipeline☆14Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated last month
- Predict MLST directly from uncorrected long reads☆27Updated 2 years ago
- Plasmid exploration of bacterial genomes☆18Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at …☆13Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 10 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 4 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Phylotype your strains using Clermont's 2013 method: ezclermont.org☆10Updated 2 years ago
- Basic workflow for nanopore sequencing data☆15Updated 2 weeks ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆43Updated this week
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 6 years ago
- UPHL's Reference Free Pipeline☆25Updated 2 weeks ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- List and download schemes from pubMLST.org and other BIGSDB servers☆8Updated 4 months ago
- Genome size estimation from long read overlaps☆48Updated 2 months ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 7 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 7 months ago
- plasmidVerify: plasmid contig verification tool☆12Updated 4 years ago
- Calculate assocations between genes and traits☆22Updated 3 months ago
- Intra-species bacterial contamination detection☆25Updated last week
- Plasmid analysis using rearrangement distances☆31Updated 3 months ago
- Assembly based core SNP alignments☆7Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated last year
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆14Updated 2 years ago
- Generation of pan-genome profile files using Roary output.☆9Updated 7 years ago