egluckthaler / starfishLinks
starfish: a modular toolkit for giant mobile element annotation
☆33Updated 10 months ago
Alternatives and similar repositories for starfish
Users that are interested in starfish are comparing it to the libraries listed below
Sorting:
- Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data☆36Updated last year
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆62Updated 2 years ago
- BEAV: Bacterial Element Annotation reVamped☆70Updated 2 months ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆67Updated 3 years ago
- A massively parallel tool for model selection and tree inference on thousands of genes☆50Updated last year
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆35Updated last month
- Bacterial GWAS analysis☆45Updated 3 months ago
- Gene-flank analysis tool☆33Updated 10 months ago
- This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MA…☆35Updated 2 years ago
- whole genome MLST analysis☆49Updated 4 months ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆75Updated last month
- A comparative genomics workflow using Nextflow, conda, Julia and R☆45Updated last year
- Bifrost graph gene caller.☆95Updated last month
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆55Updated 4 months ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Synteny Imager☆64Updated 3 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆61Updated 8 months ago
- nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…☆70Updated 3 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Read, manipulate and visualize 'Pairwise mApping Format' data in R☆74Updated 4 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- Graph-based assembly phasing☆87Updated 6 months ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Updated 2 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- ☆30Updated 2 years ago
- k-mer learning materials☆80Updated 8 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆41Updated last week
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆31Updated last month