karel-brinda / MiniPhy
Phylogenetic compression of extremely large genome collections [661k βππ²ππΆπ | BIGSIdata βπ°π΄ππΆπ | AllTheBact'23 βπ³π±ππΆπ]
β22Updated 3 months ago
Alternatives and similar repositories for MiniPhy:
Users that are interested in MiniPhy are comparing it to the libraries listed below
- A mathematically characterized hypothesis test for organism presence/absence in a metagenomeβ30Updated 2 weeks ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)β27Updated 10 months ago
- Plasmid analysis using rearrangement distancesβ33Updated 4 months ago
- Genome size estimation from long read overlapsβ50Updated 3 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomesβ15Updated 6 years ago
- β13Updated last month
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.β27Updated 3 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.β50Updated 8 months ago
- Fast and space-efficient taxonomic classification of long readsβ43Updated 2 weeks ago
- software to identify primers that can distinguish genomesβ21Updated last month
- Microbial agile accurate SNP Typerβ29Updated last year
- A pipeline for bioinformatics analysis of bacterial genomesβ19Updated 8 months ago
- Recombination-free treesβ57Updated last year
- Colinear block visualisation toolβ30Updated last year
- Code to create a PRG from a Multiple Sequence Alignment fileβ24Updated 11 months ago
- Get microbial sequence data easier and fasterβ28Updated 5 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological dataβ32Updated 3 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.β22Updated this week
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classificationβ12Updated 11 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and meβ¦β22Updated 2 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic dataβ19Updated 5 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignmentβ56Updated last week
- β10Updated 4 years ago
- Mandrake πΏ/π¨βπ¬π¦ β Fast visualisation of the population structure of pathogens using Stochastic Cluster Embeddingβ36Updated this week
- Visualize microbial evolution at the SNP level!β14Updated 3 months ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.β24Updated 2 weeks ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.β44Updated last week
- β17Updated 9 months ago
- Fast viral consensus genome reconstructionβ22Updated 2 months ago
- frame-shift correction for long-read (meta)genomicsβ33Updated last year