Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
☆188Jun 12, 2026Updated this week
Alternatives and similar repositories for taxprofiler
Users that are interested in taxprofiler are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- (Meta-)genome screening for functional and natural product gene sequences☆111Updated this week
- Assembly and binning of metagenomes☆302Updated this week
- Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.☆19Jun 3, 2025Updated last year
- Parallelised and automated construction of metagenomic classifier databases of different tools☆21Updated this week
- Amplicon sequencing analysis workflow using DADA2 and QIIME2☆250Updated this week
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.☆34May 29, 2026Updated 2 weeks ago
- nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.☆12Updated this week
- TAXnomic Profile Aggregation and STAndardisation☆44May 2, 2026Updated last month
- Pipeline to fetch metadata and raw FastQ files from public databases☆194May 29, 2026Updated 2 weeks ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆53Updated this week
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆24Apr 30, 2026Updated last month
- Assembly and intrahost/low-frequency variant calling for viral samples☆165May 13, 2026Updated last month
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆94Updated this week
- A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.☆37Jun 3, 2026Updated last week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A repo with just adapter sequences☆15Jul 7, 2025Updated 11 months ago
- Precise host read removal☆124Apr 13, 2026Updated 2 months ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆253May 13, 2026Updated last month
- Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data☆12Feb 20, 2026Updated 3 months ago
- Surveillance of pathogens using population genomics and sequencing☆60Apr 30, 2026Updated last month
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆27Feb 6, 2023Updated 3 years ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆307Feb 3, 2026Updated 4 months ago
- Nanopore demultiplexing, QC and alignment pipeline☆227Apr 30, 2026Updated last month
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆199Updated this week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A flexible pipeline for complete analysis of bacterial genomes☆517May 21, 2026Updated 3 weeks ago
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆90May 11, 2026Updated last month
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Updated this week
- Raspir, the rare species identifier☆11Oct 19, 2023Updated 2 years ago
- Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.☆179Apr 6, 2026Updated 2 months ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆179Apr 22, 2026Updated last month
- strain-level analysis tools☆41Oct 21, 2024Updated last year
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆106Updated this week
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated 11 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with…☆170Apr 22, 2026Updated last month
- A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV☆472May 28, 2026Updated 2 weeks ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆98Jun 8, 2026Updated last week
- Metagenomic classification of long-read sequencing data☆107Jan 22, 2026Updated 4 months ago
- nf-test utility functions☆12May 22, 2026Updated 3 weeks ago
- A pipeline to investigate horizontal gene transfer from NGS data☆27Apr 30, 2026Updated last month
- Simple bacterial assembly and annotation pipeline☆88Updated this week