nf-core / phyloplaceLinks
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
☆12Updated 3 weeks ago
Alternatives and similar repositories for phyloplace
Users that are interested in phyloplace are comparing it to the libraries listed below
Sorting:
- Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.☆34Updated last week
- Semi-Automatic Taxonomy Improvement and Validation Algorithm☆18Updated last year
- (Meta-)genome screening for functional and natural product gene sequences☆93Updated this week
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆115Updated last week
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆98Updated 6 months ago
- Small variant calling for haploid samples☆45Updated 2 months ago
- Simple bacterial assembly and annotation pipeline☆78Updated 3 weeks ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Updated 7 months ago
- CLI tool to annotate genes with KOfam☆85Updated 2 years ago
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆78Updated last month
- ☆50Updated 3 years ago
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆102Updated 6 months ago
- A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.☆32Updated 5 months ago
- Strain resolver for metagenomics☆78Updated last year
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads☆112Updated last year
- Graph-based assembly phasing☆87Updated 6 months ago
- Bifrost graph gene caller.☆95Updated last month
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data☆168Updated this week
- ☆84Updated 2 years ago
- A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulatio…☆114Updated 5 months ago
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆38Updated last week
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆88Updated 2 years ago
- Inference of microbial interaction networks from large-scale heterogeneous abundance data☆89Updated last month
- Massively parallel phylogenetic placement of genetic sequences☆84Updated 3 years ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆81Updated 3 weeks ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆50Updated 3 years ago
- SKESA assembler☆123Updated last year
- ☆73Updated last month
- Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake☆49Updated last year
- A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…☆59Updated 9 months ago