katholt / srst2Links
Short Read Sequence Typing for Bacterial Pathogens
☆139Updated 4 years ago
Alternatives and similar repositories for srst2
Users that are interested in srst2 are comparing it to the libraries listed below
Sorting:
- BSR-Based Allele Calling Algorithm☆148Updated 3 weeks ago
- Pan-genome wide association studies☆204Updated last year
- "Reads to report" for public health and clinical microbiology☆141Updated last year
- Antimicrobial Resistance Identification By Assembly☆180Updated 2 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆141Updated last year
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆123Updated last year
- snipit: summarise snps relative to your reference sequence☆162Updated 3 weeks ago
- A tool to circularize genome assemblies☆247Updated last year
- Metagenomic classification of long-read sequencing data☆95Updated last month
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆237Updated 2 years ago
- DAS Tool☆158Updated last year
- A user-friendly workflow for phylogenomics☆221Updated 2 months ago
- Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆205Updated last year
- Processing pipeline for pan-genome visulization and exploration☆140Updated 2 years ago
- VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data☆137Updated 5 years ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆156Updated 5 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆116Updated last year
- Convert various sequence formats to FASTA☆138Updated 3 years ago
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data☆165Updated this week
- CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…☆221Updated this week
- A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework☆112Updated 6 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆203Updated last month
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆126Updated last week
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆120Updated 2 weeks ago
- a short-read polishing tool for long-read assemblies☆193Updated 3 weeks ago
- Making whole bacterial genome sequencing data analysis easy☆112Updated 5 months ago
- Create a tree using Mash distances☆171Updated last year
- An updated pipeline for pangenome investigation☆316Updated 7 months ago
- Virus Identification By iteRative ANnoTation☆173Updated last year
- Long-read mock community experiments☆105Updated 4 years ago