LaborBerlin / ont-assembly-snake
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.
☆22Updated 10 months ago
Alternatives and similar repositories for ont-assembly-snake:
Users that are interested in ont-assembly-snake are comparing it to the libraries listed below
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆25Updated 10 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated last month
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- Recombination-free trees☆57Updated last year
- Gene-flank analysis tool☆27Updated 2 months ago
- Long read metagenomics practical at EBAME18☆18Updated 6 years ago
- tools for assessing the accuracy of genome assemblies☆34Updated 10 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- whole genome MLST analysis☆40Updated 9 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Calculate confidence scores from Kraken2 output☆21Updated last year
- Ley Lab MetaGenome Profiler DataBase generator☆49Updated 2 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆32Updated 3 months ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated this week
- ☆36Updated 2 years ago
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago
- Split Kmer Analysis☆62Updated 2 years ago
- IslandPath standalone software☆31Updated last year
- Predict MLST directly from uncorrected long reads☆27Updated 2 years ago
- Nanomotif - a tool for identifying methylated motifs in metagenomic samples☆25Updated this week
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- ☆20Updated 5 months ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago