Alternatives and similar repositories for EMIRGE

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

• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆59Updated 4 years ago
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆71Updated 5 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• rrwick / Metagenomics-Index-Correction
  ☆84Updated last year
• knights-lab / BURST
  An ultrafast optimal aligner for mapping large NGS data to large genome databases.
  ☆58Updated last year
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 4 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 2 years ago
• snacktavish / TreeToReads
  Pipeline to generate NGS reads from a phylogeny
  ☆39Updated 2 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆59Updated 6 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆46Updated 5 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆73Updated 5 years ago
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆83Updated 9 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆48Updated 3 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆76Updated 2 years ago
• katholt / RedDog
  ☆36Updated 3 years ago
• guyleonard / taxdump_edit
  Add new taxa or taxonomic groups to the NCBI Taxdump files
  ☆20Updated 5 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 4 years ago
• ryanmelnyk / PyParanoid
  Rapid and scalable homolog identification for bacterial genomes
  ☆33Updated 6 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• jhawkey / IS_mapper
  IS mapping software
  ☆56Updated 3 years ago
• thackl / minidot
  Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
  ☆76Updated 9 years ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆54Updated last year
• claczny / VizBin
  Repository of our application for human-augmented binning
  ☆28Updated 4 years ago
• MadsAlbertsen / mmgenome
  Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
  ☆27Updated 8 years ago
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆74Updated last year
• FOI-Bioinformatics / flextaxd
  FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…
  ☆67Updated 5 months ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆73Updated 3 weeks ago