christophertbrown / iRep
scripts for estimating bacteria replication rates based on population genome copy number variation
☆72Updated 5 years ago
Alternatives and similar repositories for iRep:
Users that are interested in iRep are comparing it to the libraries listed below
- GTDB taxonomy taxdump files with trackable TaxIds☆52Updated 11 months ago
- Estimate metagenomic coverage and sequence diversity☆48Updated 8 months ago
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆59Updated 5 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆44Updated 4 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- Ley Lab MetaGenome Profiler DataBase generator☆49Updated 2 years ago
- IS mapping software☆53Updated 3 years ago
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆29Updated 5 years ago
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆69Updated 9 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- ☆81Updated last year
- Improvement of metagenome-assembled genomes☆51Updated 5 years ago
- Microbial Populations as Clusters Of Gene Transfer☆44Updated last year
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆32Updated 4 years ago
- ☆50Updated last year
- A tool for removing redundant genomes from a set of assemblies☆71Updated last year
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆73Updated last year
- A toolbox for improving metagenome-assembled genomes.☆63Updated 3 years ago
- StrainFinder☆26Updated 6 years ago
- Contains a fasta format database of a large variety of mobile genetic elements and an annotation file☆46Updated 3 years ago
- ☆52Updated 3 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆54Updated 3 years ago
- a collection of scripts for organising bacterial genomes by species☆76Updated 3 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 11 months ago
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆82Updated 9 years ago
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆72Updated 2 years ago
- Convert GTDB taxonomy to NCBI taxdump format☆68Updated last year
- ☆32Updated last year
- ☆41Updated 4 years ago