snayfach / MIDASLinks
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
☆127Updated last year
Alternatives and similar repositories for MIDAS
Users that are interested in MIDAS are comparing it to the libraries listed below
Sorting:
- Long-read mock community experiments☆105Updated 3 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated 2 years ago
- ☆82Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆59Updated 5 years ago
- DDBJ Fast Annotation and Submission Tool☆79Updated last month
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆121Updated last year
- Woltka: a versatile meta'omic data classifier☆74Updated 2 months ago
- a collection of scripts for organising bacterial genomes by species☆76Updated 3 years ago
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆116Updated 3 months ago
- a signal-level demultiplexer for Oxford Nanopore reads☆126Updated 4 years ago
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆69Updated 11 months 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
- Clustering cONtigs with COverage and ComposiTion☆130Updated 5 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆72Updated 5 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆136Updated last year
- FunGAP: fungal Genome Annotation Pipeline☆111Updated last year
- Development version of Easyfig☆97Updated last year
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆74Updated 2 years ago
- A toolbox for comparative genomics.☆103Updated 4 years ago
- Software for prediction of plasmid sequences in metagenomic assemblies☆102Updated 3 years ago
- A toolbox for pangenome analysis and threshold evaluation.☆97Updated 2 years 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…☆141Updated last month
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆57Updated last year
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆127Updated 3 weeks ago
- Convert GTDB taxonomy to NCBI taxdump format☆71Updated last year
- Metatranscriptomics Tutorial☆62Updated last year
- ☆125Updated this week
- OPERA-MS - Hybrid Metagenomic Assembler☆95Updated 11 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆114Updated last year
- SHallow shOtGUN profiler☆54Updated 3 years ago