wslh-bio / spriggan
Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.
☆15Updated this week
Alternatives and similar repositories for spriggan:
Users that are interested in spriggan are comparing it to the libraries listed below
- UPHL's Reference Free Pipeline☆26Updated 3 weeks ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆56Updated last year
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆33Updated this week
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆35Updated 3 weeks ago
- Whole genome core alignments from multiple draft genomes☆12Updated 8 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Order and orientation of complete bacterial genomes☆27Updated last year
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Bacterial surveillance pipeline.☆24Updated 2 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆57Updated 3 weeks ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆48Updated 2 years ago
- whole genome MLST analysis☆41Updated last week
- Small utility script to submit genomes to PHASTER for phage detection☆24Updated 3 years ago
- Calculate assocations between genes and traits☆23Updated 3 weeks ago
- Recombination-free trees☆57Updated last week
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Gene-flank analysis tool☆27Updated 3 months ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- Intra-species bacterial contamination detection☆25Updated last month
- Bacterial genomes finishing tool for structural insights on draft genomes☆24Updated last year
- Gene Absence Presence Identification tool.☆26Updated this week
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆33Updated last month
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 5 months ago
- Bacterial taxonomy construction and evaluation in R☆13Updated last year
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆37Updated 3 months ago
- Influenza data pipeline to automate genotyping assignment☆29Updated last month
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 8 months ago
- ☆42Updated this week
- in silico typing of the H. influenzae cap locus☆11Updated 8 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆20Updated this week