GATB / simka
Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
☆47Updated 3 years ago
Alternatives and similar repositories for simka:
Users that are interested in simka are comparing it to the libraries listed below
- Estimate metagenomic coverage and sequence diversity☆48Updated 7 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- De novo Extraction of Strains from MetAgeNomes☆68Updated 4 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆43Updated 4 years ago
- Gene-flank analysis tool☆27Updated 3 months ago
- Split Kmer Analysis☆62Updated 2 years ago
- ☆80Updated last year
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆43Updated 4 years ago
- IS mapping software☆53Updated 3 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- a collection of scripts for organising bacterial genomes by species☆76Updated 3 years ago
- Bifrost graph gene caller.☆93Updated 6 months ago
- Recombination-free trees☆57Updated last year
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆48Updated 2 years ago
- ☆36Updated 2 years ago
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆57Updated 5 years ago
- ☆52Updated 3 years ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- Ley Lab MetaGenome Profiler DataBase generator☆49Updated 2 years ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆44Updated 3 months ago
- GTDB taxonomy taxdump files with trackable TaxIds☆52Updated 10 months ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆71Updated 5 years ago
- Split k-mer analysis – version 2☆75Updated last month
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆82Updated 9 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated last year
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- A tool for removing redundant genomes from a set of assemblies☆70Updated last year
- A toolbox for improving metagenome-assembled genomes.☆63Updated 3 years ago