Intra-species bacterial contamination detection
☆25Feb 5, 2026Updated last month
Alternatives and similar repositories for ConFindr
Users that are interested in ConFindr are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 5 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆13Jun 30, 2023Updated 2 years ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 4 years ago
- A taxonomic classifier of plasmids☆29Jul 7, 2021Updated 4 years ago
- Assemble bacterial isolate genomes from Nanopore reads☆129Jan 22, 2025Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated 3 weeks ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆14Aug 26, 2024Updated last year
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆171Apr 16, 2025Updated 11 months ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Aug 5, 2022Updated 3 years ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- Assembly of Nanopore Sequencing☆17Jan 8, 2026Updated 2 months ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated last month
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 8 months ago
- UPHL's Reference Free Pipeline☆27Updated this week
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- A pipeline for whole genome assembly☆16Apr 21, 2022Updated 3 years ago
- ☆10Jul 23, 2020Updated 5 years ago
- Rapid determination of appropriate reference genomes.☆100Jan 22, 2025Updated last year
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆53Jul 24, 2025Updated 7 months 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 2 years ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆191Mar 6, 2026Updated 2 weeks ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆14Jun 12, 2024Updated last year
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆39Feb 1, 2023Updated 3 years ago
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆12Dec 2, 2024Updated last year
- Plasmid and antimicrobial resistance pipeline☆16Dec 30, 2024Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Dec 11, 2020Updated 5 years ago
- BSR-Based Allele Calling Algorithm☆148Mar 13, 2026Updated last week
- Predict plasmids from uncorrected long read data☆41Feb 27, 2026Updated 3 weeks ago