christophertbrown / iRep
scripts for estimating bacteria replication rates based on population genome copy number variation
☆68Updated 4 years ago
Related projects ⓘ
Alternatives and complementary repositories for iRep
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆43Updated 4 years ago
- ☆78Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆56Updated 5 years ago
- A tool for removing redundant genomes from a set of assemblies☆68Updated last year
- IS mapping software☆51Updated 2 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 3 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆43Updated last year
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆69Updated 4 months ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆47Updated 2 years ago
- A toolbox for comparative genomics.☆97Updated 3 years ago
- a collection of scripts for organising bacterial genomes by species☆76Updated 2 years ago
- Convert GTDB taxonomy to NCBI taxdump format☆66Updated last year
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆27Updated 4 years ago
- GraftM - Rapid community profiles from metagenomes☆44Updated 3 months ago
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆31Updated 4 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆42Updated 4 years ago
- Improvement of metagenome-assembled genomes☆49Updated 4 years ago
- GTDB taxonomy taxdump files with trackable TaxIds☆48Updated 6 months ago
- ☆51Updated 3 years ago
- Prediction of prophages from bacterial genomes☆70Updated 11 months ago
- StrainFinder☆27Updated 6 years ago
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆70Updated last year
- Split Kmer Analysis☆63Updated 2 years ago
- Microbial Populations as Clusters Of Gene Transfer☆42Updated 11 months ago
- Estimate metagenomic coverage and sequence diversity☆46Updated 3 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated last year
- Recovery of prokaryotic genomes from shotgun metagenomic sequencing data☆56Updated 3 years ago
- ☆45Updated 6 months ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆41Updated last year
- Add new taxa or taxonomic groups to the NCBI Taxdump files☆19Updated 4 years ago