[Archived] SnakeMake pipeline to run BlobTools on public assemblies
☆11Jul 3, 2023Updated 2 years ago
Alternatives and similar repositories for pipeline
Users that are interested in pipeline are comparing it to the libraries listed below
Sorting:
- ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples fro…☆13Feb 13, 2023Updated 3 years ago
- ☆14Dec 23, 2025Updated 2 months ago
- An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter☆14Jan 18, 2019Updated 7 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Mar 12, 2024Updated last year
- Nextflow workflow for automatic repeat detection, classification and masking☆13Feb 19, 2018Updated 8 years ago
- CLI to automate Nextflow pipeline testing☆12Dec 15, 2025Updated 2 months ago
- A collection of Groovy classes that provide utility services to nextflow pipelines.☆13Oct 25, 2022Updated 3 years ago
- ☆11Mar 5, 2025Updated 11 months ago
- Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.☆15Feb 12, 2026Updated 2 weeks ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Mar 7, 2025Updated 11 months ago
- A Nextflow pipeline for running synteny analysis.☆16Jun 17, 2025Updated 8 months ago
- VCF Observer is a VCF file analysis, comparison, and visualization tool.☆18Jan 3, 2025Updated last year
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆27Jul 21, 2025Updated 7 months ago
- Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.☆25Feb 11, 2026Updated 2 weeks ago
- Neptune: Genomic Signature Discovery☆21Nov 20, 2024Updated last year
- WGS (Wheat) Robust Assembly Pipeline☆22Sep 4, 2021Updated 4 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
- Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.☆26Oct 24, 2025Updated 4 months ago
- A Python package for gene-centric taxonomic and functional classification using phylogenetic placement☆26Sep 3, 2024Updated last year
- From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)☆21Jul 8, 2024Updated last year
- Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads☆32Nov 20, 2025Updated 3 months ago
- DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets☆30Jul 3, 2023Updated 2 years ago
- ☆33Feb 21, 2026Updated last week
- ☆33Jul 9, 2024Updated last year
- ☆25Oct 26, 2021Updated 4 years ago
- frame-shift correction for long-read (meta)genomics☆33Dec 11, 2023Updated 2 years ago
- Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes☆31Feb 10, 2026Updated 2 weeks ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 8 months ago
- Lint Nextflow pipelines in Python.☆11Jan 23, 2025Updated last year
- This bartender version could handle arbitrary length of barcode☆32Jan 6, 2024Updated 2 years ago
- We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a …☆32Jan 3, 2022Updated 4 years ago
- TELR is a fast non-reference transposable element detector from long read sequencing data.☆35Jul 27, 2023Updated 2 years ago
- Differential gene expression analysis and pathway analysis of RNAseq data☆32Jul 3, 2025Updated 7 months ago
- Phasing of dikaryotic fungal genome assemblies☆13Mar 1, 2023Updated 3 years ago
- ☆14Mar 22, 2018Updated 7 years ago
- A tool for recovering synteny blocks from multiple alignment☆32Oct 18, 2021Updated 4 years ago
- Nextflow language support for Visual Studio Editor☆37Feb 16, 2026Updated last week
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- A python library for generating a clustered heatmap with dendrograms.☆34Mar 17, 2022Updated 3 years ago