staphopia / staphopia-sccmec
Archived - please see updated sccmec tool at link below
☆13Updated 8 months ago
Alternatives and similar repositories for staphopia-sccmec
Users that are interested in staphopia-sccmec are comparing it to the libraries listed below
Sorting:
- List and download schemes from pubMLST.org and other BIGSDB servers☆10Updated 7 months ago
- Plasmid exploration of bacterial genomes☆18Updated 3 years ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated 2 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆28Updated this week
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆25Updated 7 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated 3 weeks ago
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 7 years ago
- Intra-species bacterial contamination detection☆25Updated 3 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆34Updated last month
- plasmidVerify: plasmid contig verification tool☆13Updated 5 years ago
- Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at …☆13Updated 3 years ago
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago
- Basic workflow for nanopore sequencing data☆16Updated 3 weeks ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Assembly based core SNP alignments☆7Updated 2 years ago
- in silico typing of the H. influenzae cap locus☆12Updated 10 months ago
- mGEMS Genomic epidemiology with mixed samples☆16Updated 8 months ago
- Calculate assocations between genes and traits☆23Updated 2 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆51Updated last month
- Order and orientation of complete bacterial genomes☆27Updated last year
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated 2 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- UPHL's Reference Free Pipeline☆26Updated last week
- Generation of pan-genome profile files using Roary output.☆9Updated 7 years ago
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago