SionBayliss / PIRATE
A toolbox for pangenome analysis and threshold evaluation.
☆92Updated 2 years ago
Alternatives and similar repositories for PIRATE:
Users that are interested in PIRATE are comparing it to the libraries listed below
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆113Updated last month
- SKESA assembler☆113Updated 3 months ago
- A toolbox for comparative genomics.☆99Updated 3 years ago
- DDBJ Fast Annotation and Submission Tool☆78Updated 3 weeks ago
- a collection of scripts for organising bacterial genomes by species☆76Updated 2 years ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆71Updated last year
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆111Updated 7 months ago
- Reorients assembled microbial sequences☆106Updated this week
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆114Updated last year
- ☆79Updated last year
- Interactive quality assessment of genome assemblies☆91Updated last week
- IS mapping software☆53Updated 3 years ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆72Updated 4 months ago
- Sorts amplicons from Nanopore sequencing data based on similarity☆33Updated 3 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆87Updated this week
- Create a tree using Mash distances☆157Updated last year
- A hybrid assembly and MAG recovery pipeline (and more!)☆85Updated this week
- Metagenomic classification of long-read sequencing data☆69Updated last month
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆81Updated last year
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆69Updated 7 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆94Updated this week
- Pairwise SNP distance matrix from a FASTA sequence alignment☆128Updated 10 months ago
- Foreign Contamination Screening caller scripts and documentation☆111Updated last month
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆87Updated last year
- Making whole bacterial genome sequencing data analysis easy☆102Updated 2 months ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆132Updated last month
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆110Updated last week
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆28Updated 4 years ago
- CDCgov/mycosnp-nf☆42Updated 3 weeks ago
- Synteny Imager☆60Updated 4 months ago