Saskia-Oosterbroek / deconaView external linksLinks
fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
☆50Sep 24, 2025Updated 4 months ago
Alternatives and similar repositories for decona
Users that are interested in decona are comparing it to the libraries listed below
Sorting:
- ☆31May 29, 2024Updated last year
- Reference-free clustering and consensus forming of long-read amplicon sequencing☆65Apr 21, 2025Updated 9 months ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆13Jun 12, 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
- A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework☆117Jan 8, 2026Updated last month
- 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
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆55Oct 24, 2025Updated 3 months ago
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆18Apr 4, 2023Updated 2 years ago
- creating reference databases for amplicon sequencing☆48Jan 13, 2026Updated last month
- Sorts amplicons from Nanopore sequencing data based on similarity☆41Oct 9, 2025Updated 4 months ago
- Tutorial for Metagenomics Analyses☆10Jun 16, 2020Updated 5 years ago
- MetaPORE – Chiu Laboratory, University of California, San Francisco☆12Nov 4, 2015Updated 10 years ago
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆13Feb 9, 2025Updated last year
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Jun 30, 2023Updated 2 years ago
- Quality control plotting for long reads☆10May 14, 2024Updated last year
- A simple fastp-MultiQC nextflow pipeline☆12Feb 2, 2023Updated 3 years ago
- Course materials for an introduction to SARS-CoV-2 sequencing data analysis☆14Aug 15, 2024Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆32Feb 9, 2026Updated last week
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.☆17Jul 31, 2025Updated 6 months ago
- Nanopore Real-Time Analysis Tool☆17Sep 4, 2024Updated last year
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆55Jun 14, 2025Updated 8 months ago
- Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method☆17Dec 29, 2022Updated 3 years ago
- A Shotgun Metagenome Annotation Pipeline☆24Mar 24, 2017Updated 8 years ago
- ☆14Jun 30, 2021Updated 4 years ago
- Organism-specific interpretation of AMR genotypes☆15Mar 13, 2024Updated last year
- Stitch together Nanopore tiled amplicon data without polishing a reference☆17Jan 29, 2024Updated 2 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Apr 26, 2025Updated 9 months ago
- ☆19Dec 4, 2025Updated 2 months ago
- Real-time analysis pipeline for nanopore 16S rRNA data☆15Nov 29, 2022Updated 3 years ago
- MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read M…☆13Jul 2, 2022Updated 3 years ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Dec 11, 2020Updated 5 years ago
- Assembly of Nanopore Sequencing☆17Jan 8, 2026Updated last month
- Look Up Guild Information for Fungi in R☆23Mar 20, 2025Updated 10 months ago
- finding conserved regions in highly diverse genomes☆15Jun 1, 2025Updated 8 months ago
- ☆19Updated this week
- A simple pipeline for bacterial assembly and quality control☆16Jan 30, 2026Updated 2 weeks ago
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads☆114Nov 20, 2023Updated 2 years ago