Alternatives and similar repositories for MIDAS

Users that are interested in MIDAS are comparing it to the libraries listed below

• rrwick / Metagenomics-Index-Correction
  ☆84Updated 2 years ago
• LomanLab / mockcommunity
  Long-read mock community experiments
  ☆105Updated 4 years ago
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆141Updated 2 years ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆83Updated last month
• BinPro / CONCOCT
  Clustering cONtigs with COverage and ComposiTion
  ☆134Updated 5 years ago
• DiltheyLab / MetaMaps
  Long-read metagenomic analysis
  ☆106Updated 2 years ago
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆129Updated last year
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆120Updated last month
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆58Updated last year
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆61Updated 6 years ago
• nick-youngblut / gtdb_to_taxdump
  Convert GTDB taxonomy to NCBI taxdump format
  ☆73Updated 2 years ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆66Updated 2 years ago
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• marbl / parsnp
  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 3 weeks ago
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago
• EBI-Metagenomics / emg-viral-pipeline
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  ☆144Updated last week
• khyox / recentrifuge
  Recentrifuge: robust comparative analysis and contamination removal for metagenomics
  ☆98Updated 5 months ago
• FOI-Bioinformatics / flextaxd
  FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…
  ☆67Updated 7 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• fanglab / nanodisco
  nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…
  ☆70Updated 3 years ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆142Updated last year
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆113Updated 6 months ago
• mjsull / Easyfig
  Development version of Easyfig
  ☆100Updated last year
• mgalardini / pyseer
  SEER, reimplemented in python 🐍🔮
  ☆125Updated 5 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆81Updated 3 years ago
• microgenomics / tutorials
  In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given…
  ☆84Updated 7 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆116Updated last year
• genomehubs / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆113Updated 5 months ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆56Updated last year
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆55Updated 3 years ago