snayfach / MIDASLinks
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
☆130Updated 2 years ago
Alternatives and similar repositories for MIDAS
Users that are interested in MIDAS are comparing it to the libraries listed below
Sorting:
- Convert GTDB taxonomy to NCBI taxdump format☆72Updated 2 years ago
- ☆84Updated 2 years ago
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆61Updated 6 years ago
- Processing pipeline for pan-genome visulization and exploration☆142Updated 2 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆66Updated 2 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆143Updated last year
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆129Updated last year
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆59Updated last year
- DDBJ Fast Annotation and Submission Tool☆83Updated 2 months ago
- Long-read mock community experiments☆104Updated 4 years ago
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆82Updated 9 years ago
- Clustering cONtigs with COverage and ComposiTion☆135Updated 5 years ago
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆121Updated 3 weeks ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆146Updated last month
- Long-read metagenomic analysis☆106Updated 2 years ago
- viralVerify: viral contig verification tool☆72Updated 4 years ago
- Rapid and scalable correlation estimation for compositional data☆95Updated last year
- VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies☆144Updated 3 weeks ago
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆124Updated 2 years ago
- "Reads to report" for public health and clinical microbiology☆141Updated last year
- ONT assembly and Illumina polishing pipeline☆89Updated 4 years ago
- SURPI☆86Updated 9 years ago
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆99Updated 6 months ago
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆79Updated 2 years ago
- a signal-level demultiplexer for Oxford Nanopore reads☆126Updated 4 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆72Updated 5 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆56Updated 3 years ago
- Development version of Easyfig☆102Updated last year
- GTDB taxonomy taxdump files with trackable TaxIds☆55Updated 6 months ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago