nf-core / phyloplaceLinks
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
☆12Updated 2 months 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.☆33Updated 2 months ago
- Semi-Automatic Taxonomy Improvement and Validation Algorithm☆20Updated 2 years ago
- (Meta-)genome screening for functional and natural product gene sequences☆101Updated last week
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆99Updated last month
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆121Updated 3 weeks ago
- Massively parallel phylogenetic placement of genetic sequences☆86Updated 3 years ago
- CLI tool to annotate genes with KOfam☆88Updated 2 years ago
- SKESA assembler☆124Updated last year
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Updated 10 months ago
- A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.☆33Updated 8 months ago
- Bifrost graph gene caller.☆98Updated 3 weeks ago
- Small variant calling for haploid samples☆48Updated last month
- A pipeline for running AMRfinderPlus and collating results into functional classes☆91Updated 2 months ago
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data☆177Updated last week
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆86Updated this week
- ARG normalization by mapping to the ARO ontology.☆62Updated 6 months ago
- Simple bacterial assembly and annotation pipeline☆81Updated 2 weeks ago
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆89Updated 2 years ago
- Strain resolver for metagenomics☆80Updated last year
- A toolbox for pangenome analysis and threshold evaluation.☆99Updated 3 years ago
- REference Sequence annotation and CuRatIon Pipeline☆98Updated this week
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆120Updated last year
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads☆114Updated 2 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆63Updated 3 weeks ago
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆103Updated last week
- Using ggtree to build phylogenetic trees☆50Updated last year
- A toolbox for comparative genomics.☆108Updated 4 years ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆65Updated 2 months ago
- ☆84Updated 2 years ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆51Updated 4 years ago