Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.
☆29May 7, 2026Updated 3 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. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆28May 7, 2026Updated 3 months ago
- ☆36Updated this week
- A tool for generating consensus long-read assemblies for bacterial genomes☆236Updated this week
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated this week
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆154Jul 24, 2026Updated 3 weeks ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Apr 30, 2026Updated 3 months ago
- detect temperate phage (active prophage) in assembled bacterial genome sequences☆15Feb 10, 2022Updated 4 years ago
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆24Jul 28, 2026Updated 2 weeks ago
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated last year
- High-quality Nanopore-only genome polisher☆71Aug 16, 2024Updated last year
- Inferring global and local strict molecular clocks using root-to-tip regression☆20Jun 30, 2026Updated last month
- PuntSeq - Chasing the microbial diversity of Cambridge's freshwater☆20Nov 12, 2020Updated 5 years ago
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆82Sep 20, 2023Updated 2 years ago
- A pipeline for whole genome assembly☆16Apr 21, 2022Updated 4 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- Run multiple programs to check if a VCF is usable☆11May 15, 2020Updated 6 years ago
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆66Jan 22, 2026Updated 6 months ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆55Jul 24, 2025Updated last year
- A Nextflow pipeline for genome and pan-genome annotation☆16Feb 22, 2026Updated 5 months ago
- A new high-resolution long-read metagenome assembler for even noisy reads☆163Jul 3, 2026Updated last month
- blastn2dotplots: multiple dot-plot visualizer☆29Sep 15, 2025Updated 11 months ago
- A tool for drawing ANI clustermap between all-vs-all microbial genomes☆94May 3, 2025Updated last year
- A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.☆36Apr 4, 2025Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆50Feb 20, 2026Updated 5 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆24Sep 12, 2025Updated 11 months ago
- Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads☆51Aug 3, 2026Updated last week
- GTDB taxonomy taxdump files with trackable TaxIds☆62Apr 18, 2026Updated 3 months ago
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆26May 8, 2024Updated 2 years ago
- Scripts for analyses in the Griffin manuscript☆12Dec 14, 2022Updated 3 years ago
- Benchmarking of long-read assembly tools for bacterial whole genomes☆172Mar 15, 2021Updated 5 years ago
- Realtime base modification frequency tool☆13Sep 16, 2025Updated 10 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Protobuff and gRPC specifications for the MinKNOW LIMS Interface☆13Apr 20, 2021Updated 5 years ago
- A simple script to run an alignment with nucmer and visualise its results.☆10Apr 17, 2023Updated 3 years ago
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 8 months ago
- Giraffe_View is designed to help assess and visualize the accuracy of long-read sequencing datasets.☆13Sep 3, 2024Updated last year
- Scripts for file processing and analysis in phylogenetics and phylogeography☆14Jan 6, 2021Updated 5 years ago
- Assemble bacterial isolate genomes from Nanopore reads☆136Jan 22, 2025Updated last year
- Structural Variant Identification Method using Long Reads☆184Jun 29, 2021Updated 5 years ago