LaborBerlin / ont-assembly-snakeView external linksLinks
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.
☆27Apr 23, 2024Updated last year
Alternatives and similar repositories for ont-assembly-snake
Users that are interested in ont-assembly-snake are comparing it to the libraries listed below
Sorting:
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Apr 5, 2024Updated last year
- A tool for generating consensus long-read assemblies for bacterial genomes☆216Feb 4, 2026Updated last week
- A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.☆36Apr 4, 2025Updated 10 months ago
- A deep learning-based SNP calling method to identify SNPs based on low-coverage Nanopore sequencing reads.☆21Nov 20, 2022Updated 3 years ago
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆64Jan 22, 2026Updated 3 weeks ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆23Sep 12, 2025Updated 5 months ago
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated last year
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆24Nov 20, 2025Updated 2 months ago
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 2 months ago
- Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat☆25May 10, 2025Updated 9 months ago
- Analysis of sequencing error profile for long read data.☆13Mar 30, 2023Updated 2 years ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Jun 30, 2023Updated 2 years ago
- ☆10Feb 20, 2024Updated last year
- detect temperate phage (active prophage) in assembled bacterial genome sequences☆14Feb 10, 2022Updated 4 years ago
- A python tool to detect internal tandem duplication with robust variant allele frequency estimation☆12Feb 3, 2026Updated last week
- consensus approach for community profiling with nanopore amplicon sequencing data☆15Sep 30, 2024Updated last year
- High-quality Nanopore-only genome polisher☆69Aug 16, 2024Updated last year
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆146Jan 9, 2026Updated last month
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆80Sep 20, 2023Updated 2 years ago
- A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)☆11Jan 7, 2024Updated 2 years ago
- ☆10Jun 21, 2015Updated 10 years ago
- Giraffe_View is designed to help assess and visualize the accuracy of long-read sequencing datasets.☆13Sep 3, 2024Updated last year
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated 7 months ago
- A read alignment visualization library for long reads☆10Aug 6, 2022Updated 3 years ago
- Scripts for analyses in the Griffin manuscript☆11Dec 14, 2022Updated 3 years ago
- Run multiple programs to check if a VCF is usable☆11May 15, 2020Updated 5 years ago
- blastn2dotplots: multiple dot-plot visualizer☆24Sep 15, 2025Updated 4 months ago
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Jul 30, 2024Updated last year
- ☆29Aug 1, 2023Updated 2 years ago
- SNP-Assisted SV Calling and Phasing Using ONT☆25Jul 9, 2023Updated 2 years ago
- A tool for drawing ANI clustermap between all-vs-all microbial genomes☆91May 3, 2025Updated 9 months ago
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆12Dec 2, 2024Updated last year
- MEM mapper prototype☆13Nov 28, 2020Updated 5 years ago
- Generating UTRs from SHort Reads☆11Sep 28, 2020Updated 5 years ago
- Genome Assembly Validation via Inter-SUNK distances in ONT reads☆15Feb 20, 2023Updated 2 years ago
- Realtime base modification frequency tool☆13Sep 16, 2025Updated 4 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…☆51Jul 24, 2025Updated 6 months ago