Alternatives and similar repositories for pyseer

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

• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆127Updated last year
• lskatz / mashtree
  Create a tree using Mash distances
  ☆170Updated last year
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated last month
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆50Updated last year
• genomehubs / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆107Updated 4 months ago
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆100Updated 3 years ago
• fmalmeida / bacannot
  Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
  ☆103Updated 5 months ago
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆86Updated 2 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆115Updated last year
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆94Updated last week
• khyox / recentrifuge
  Recentrifuge: robust comparative analysis and contamination removal for metagenomics
  ☆98Updated 4 months ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆65Updated 4 months ago
• genomicsITER / NanoCLUST
  NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  ☆111Updated last year
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆140Updated last year
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆140Updated last year
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆174Updated 4 months ago
• snayfach / MIDAS
  An integrated pipeline for estimating strain-level genomic variation from metagenomic data
  ☆129Updated last year
• kjolley / BIGSdb
  Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
  ☆71Updated last week
• art-egorov / lovis4u
  Bioinformatics tool for Locus Visualisation
  ☆122Updated 4 months ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆119Updated this week
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• EBI-Metagenomics / emg-viral-pipeline
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  ☆140Updated last week
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆74Updated last year
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆60Updated 6 years ago
• rrwick / Metagenomics-Index-Correction
  ☆83Updated 2 years ago
• ablab / viralVerify
  viralVerify: viral contig verification tool
  ☆72Updated 4 years ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated 2 years ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆82Updated last week