Alternatives and similar repositories for amr_curation

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

• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆81Updated 3 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆62Updated 6 years ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated this week
• jhawkey / IS_mapper
  IS mapping software
  ☆57Updated 4 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆73Updated 5 years ago
• connor-lab / ncov2019-artic-nf
  A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…
  ☆91Updated 2 years ago
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆101Updated 3 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆79Updated 2 years ago
• DiltheyLab / MetaMaps
  Long-read metagenomic analysis
  ☆107Updated 2 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• snayfach / MIDAS
  An integrated pipeline for estimating strain-level genomic variation from metagenomic data
  ☆131Updated 2 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆51Updated 3 years ago
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆129Updated last year
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆48Updated 6 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆114Updated 7 months ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆117Updated last year
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆106Updated 10 months ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆75Updated last year
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆83Updated 3 months ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆86Updated 3 years ago
• kjolley / BIGSdb
  Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
  ☆73Updated this week
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆60Updated last year
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆107Updated 4 years ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆65Updated 7 months ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆60Updated last year
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• fwhelan / coinfinder
  A tool for the identification of coincident (associating and dissociating) genes in pangenomes.
  ☆108Updated 2 years ago
• lmrodriguezr / enveomics
  Scripts and libraries for Environmental Genomics
  ☆38Updated 10 months ago
• mgalardini / pyseer
  SEER, reimplemented in python 🐍🔮
  ☆125Updated 6 months ago