snayfach / MIDAS
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
☆126Updated last year
Alternatives and similar repositories for MIDAS:
Users that are interested in MIDAS are comparing it to the libraries listed below
- a signal-level demultiplexer for Oxford Nanopore reads☆125Updated 4 years ago
- Long-read mock community experiments☆104Updated 3 years ago
- DDBJ Fast Annotation and Submission Tool☆79Updated last month
- OPERA-MS - Hybrid Metagenomic Assembler☆92Updated 8 months 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…☆138Updated 2 months ago
- ☆80Updated last year
- Metagenomic classification of long-read sequencing data☆77Updated last week
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆113Updated 3 weeks ago
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆57Updated 5 years ago
- Benchmarking of long-read assembly tools for bacterial whole genomes☆170Updated 4 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆132Updated last year
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆121Updated 2 weeks ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆57Updated last year
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated last year
- FunGAP: fungal Genome Annotation Pipeline☆109Updated last year
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆120Updated last year
- Clustering cONtigs with COverage and ComposiTion☆128Updated 5 years ago
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆116Updated last year
- Rapid and scalable correlation estimation for compositional data☆85Updated 10 months ago
- Bioinformatics program inStrain☆161Updated last week
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆114Updated 10 months ago
- Convert GTDB taxonomy to NCBI taxdump format☆67Updated last year
- scripts for estimating bacteria replication rates based on population genome copy number variation☆71Updated 5 years ago
- Scripts and tutorials on how to assemble individual microbial genomes from metagenomes☆80Updated 8 years ago
- Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆197Updated 7 months ago
- SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension☆46Updated 4 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆52Updated 3 years ago
- Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing☆115Updated 10 months ago
- Development version of Easyfig☆93Updated last year
- A tool for the identification of coincident (associating and dissociating) genes in pangenomes.☆98Updated last year