matthiasblanke / App-SpaMLinks
Alignment-free Phylogenetic Placement using filtered SPAced word Matches
☆12Updated 2 years ago
Alternatives and similar repositories for App-SpaM
Users that are interested in App-SpaM are comparing it to the libraries listed below
Sorting:
- Recombination-free trees☆60Updated 2 months ago
 - Gene-flank analysis tool☆33Updated 10 months ago
 - Contains the code and workflow for the bacterial strain definition paper with Kostas Kostantinidis☆13Updated last year
 - Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 6 months ago
 - Plasmid analysis using rearrangement distances☆46Updated last month
 - Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
 - Split Kmer Analysis☆65Updated 3 years ago
 - A resistome profiler for Graphing Resistance Out Of meTagenomes☆65Updated 5 years ago
 - Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆39Updated last year
 - reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
 - ☆30Updated 2 years ago
 - Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
 - Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 7 months ago
 - Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
 - a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
 - De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
 - Bifrost graph gene caller.☆95Updated last month
 - Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆43Updated 7 months ago
 - a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 4 months ago
 - A pipeline for bioinformatics analysis of bacterial genomes☆30Updated this week
 - mGEMS Genomic epidemiology with mixed samples☆15Updated last year
 - Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆50Updated 3 years ago
 - a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
 - Order and orientation of complete bacterial genomes☆29Updated 3 months ago
 - Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
 - Code to create a PRG from a Multiple Sequence Alignment file☆25Updated last month
 - Mapping-Assisted Targeted-Assembly for Metagenomics☆23Updated 7 months ago
 - A tool for removing redundant genomes from a set of assemblies☆77Updated last month
 - Identify phage regions in bacterial genomes for masking purposes☆34Updated 6 years ago
 - Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago