snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.
☆14May 12, 2024Updated last year
Alternatives and similar repositories for snpless-nf
Users that are interested in snpless-nf are comparing it to the libraries listed below
Sorting:
- A tooL for Prokaryotic Phylogeny And Clustering Analysis☆13Jul 28, 2025Updated 7 months ago
- Three bacterial GWAS methods all rolled into one easy-to-use R package☆22Apr 16, 2024Updated last year
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- For when you just need a coverage plot.☆11Mar 26, 2021Updated 4 years ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Sep 12, 2024Updated last year
- AMR/VF LGT focused bacterial genomics analysis workflow☆28Feb 19, 2026Updated last week
- Quickly generate consensus assemblies for bacterial genomes☆14Sep 12, 2025Updated 5 months ago
- LMS algorithm for computing edit distance with SIMD optimizations☆11Mar 25, 2024Updated last year
- Microbial agile accurate SNP Typer☆30Dec 27, 2023Updated 2 years ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆13Jun 12, 2024Updated last year
- snakemake-powered cli to download genomes using NCBI datasets☆14Aug 14, 2025Updated 6 months ago
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated last year
- Nucmer from Mummer3 followed by ggplot for nicer and more customisable genome alignment plots.☆11Feb 25, 2021Updated 5 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Mar 12, 2024Updated last year
- Cookiecutter profile for making a NextFlow-based bioinformatics tool☆17Jul 8, 2024Updated last year
- A repo with just adapter sequences☆15Jul 7, 2025Updated 7 months ago
- Host depletion optimised for clinical metagenomic sequencing applications☆16Nov 18, 2024Updated last year
- A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research☆19Jan 8, 2026Updated last month
- The Metagenomics-Toolkit is a scalable, data agnostic workflow that automates the analysis of short and long metagenomic reads obtained f…☆23Updated this week
- Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.☆15Updated this week
- Experimental plugin to integrate GPT like prompt into Nextflow☆17Apr 15, 2024Updated last year
- Infer transmission clusters from SNP and timing data☆16May 20, 2020Updated 5 years ago
- µbinfie blog☆19Jul 21, 2025Updated 7 months ago
- Basecalling configuration prediction through FASTQ files☆33Nov 24, 2025Updated 3 months ago
- Organism-specific interpretation of AMR genotypes☆15Mar 13, 2024Updated last year
- Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs☆41Sep 29, 2025Updated 5 months ago
- Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments☆48Oct 15, 2025Updated 4 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Apr 26, 2025Updated 10 months ago
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 3 months ago
- ☆26Updated this week
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆17Jan 13, 2026Updated last month
- StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.☆17Dec 9, 2025Updated 2 months ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated last year
- Customer workshop materials☆19May 11, 2023Updated 2 years ago
- ☆17Jul 27, 2023Updated 2 years ago
- A simple pipeline for bacterial assembly and quality control☆16Updated this week
- kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more☆45Nov 5, 2025Updated 4 months ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆42Sep 3, 2024Updated last year