katholt / srst2
Short Read Sequence Typing for Bacterial Pathogens
☆125Updated 3 years ago
Related projects ⓘ
Alternatives and complementary repositories for srst2
- BSR-Based Allele Calling Algorithm☆134Updated 2 weeks ago
- "Reads to report" for public health and clinical microbiology☆136Updated 8 months ago
- ☆116Updated this week
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆124Updated last month
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆110Updated last year
- An updated pipeline for pangenome investigation☆269Updated last month
- Pan-genome wide association studies☆150Updated 5 months ago
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆110Updated last week
- snipit: summarise snps relative to your reference sequence☆149Updated last week
- A tool for generating consensus long-read assemblies for bacterial genomes☆308Updated 5 months ago
- CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…☆194Updated 3 weeks ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆127Updated 8 months ago
- DAS Tool☆140Updated 6 months ago
- Scan contig files against PubMLST typing schemes☆201Updated 2 years ago
- Antimicrobial Resistance Identification By Assembly☆172Updated last year
- A tool to circularize genome assemblies☆233Updated 7 months ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆214Updated last year
- Bacterial ribosomal RNA predictor☆226Updated last year
- fast phage annotation program☆148Updated this week
- Application and Python module for average nucleotide identity analyses of microbes.☆197Updated last month
- quality filtering tool for long reads☆291Updated last year
- HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.☆128Updated last year
- Software for prediction of plasmid sequences in metagenomic assemblies☆98Updated 3 years ago
- Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics☆178Updated last month
- Rapid comparison and dereplication of genomes☆263Updated this week
- Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆192Updated 3 months ago
- Processing pipeline for pan-genome visulization and exploration☆134Updated last year
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data☆128Updated 2 weeks ago
- Convert various sequence formats to FASTA☆127Updated 2 years ago
- Assessing the quality of metagenome-derived genome bins using machine learning☆173Updated 5 months ago