neherlab / pangraphLinks
A bioinformatic toolkit to align genome assemblies into pangenome graphs
☆114Updated 2 weeks ago
Alternatives and similar repositories for pangraph
Users that are interested in pangraph are comparing it to the libraries listed below
Sorting:
- Split k-mer analysis – version 2☆92Updated 2 months ago
- CLI tool to annotate genes with KOfam☆86Updated 2 years ago
- Bifrost graph gene caller.☆95Updated 2 weeks ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆100Updated 2 months ago
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆102Updated 6 months ago
- a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference☆79Updated 2 weeks ago
- Precise host read removal☆105Updated last month
- Strain resolver for metagenomics☆78Updated last year
- FastOMA is a scalable software package to infer orthology relationship.☆83Updated this week
- Efficient phylogenetic tree inference for massive taxonomic datasets☆125Updated 6 months ago
- Small variant calling for haploid samples☆43Updated last month
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆49Updated 3 years ago
- Protein hint generation pipeline for gene finding in eukaryotic genomes☆60Updated last year
- SEER, reimplemented in python 🐍🔮☆124Updated 4 months ago
- Taxonomic classifier for sequencing reads (bulk and single-cell data, short and long read) using FM-index with run-block compressed BWT.☆67Updated 3 weeks ago
- ARG normalization by mapping to the ARO ontology.☆59Updated 2 months ago
- hecatomb is a virome analysis pipeline for analysis of Illumina sequence data☆59Updated 2 weeks ago
- (Meta-)genome screening for functional and natural product gene sequences☆92Updated last week
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆116Updated last year
- Graph-based assembly phasing☆87Updated 5 months ago
- Interactive quality assessment of genome assemblies☆109Updated 5 months ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Updated last year
- Simple bacterial assembly and annotation pipeline☆78Updated last month
- Follow up to Grace Blackwell's 661k dataset, for 2023☆124Updated last month
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments☆106Updated last year
- Microbiome classification pipeline☆65Updated 4 months ago
- A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category☆71Updated 5 months ago
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆75Updated 2 weeks ago