wslh-bio / sprigganLinks
Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.
☆16Updated this week
Alternatives and similar repositories for spriggan
Users that are interested in spriggan are comparing it to the libraries listed below
Sorting:
- UPHL's Reference Free Pipeline☆26Updated 3 weeks ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆56Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Updated last month
- Whole genome core alignments from multiple draft genomes☆13Updated 8 years ago
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆35Updated 2 weeks ago
- Bacterial surveillance pipeline.☆24Updated 3 weeks 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☆29Updated 3 weeks ago
- whole genome MLST analysis☆43Updated 2 months ago
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆38Updated last month
- Small utility script to submit genomes to PHASTER for phage detection☆24Updated 3 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆36Updated 2 weeks ago
- Calculate assocations between genes and traits☆23Updated 2 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated 3 months ago
- Intra-species bacterial contamination detection☆25Updated 3 months ago
- SC2 variant detection and composition pipeline☆17Updated last year
- Gene Absence Presence Identification tool.☆26Updated 2 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆36Updated 6 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 7 months ago
- Basic workflow for nanopore sequencing data☆16Updated this week
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Recombination-free trees☆58Updated 2 months ago
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Updated 2 years ago
- ☆36Updated 3 years ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆49Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆22Updated 2 years ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆28Updated last month