Alternatives and similar repositories for pyseer

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

• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆89Updated this week
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆126Updated last year
• khyox / recentrifuge
  Recentrifuge: robust comparative analysis and contamination removal for metagenomics
  ☆94Updated 3 months ago
• lskatz / mashtree
  Create a tree using Mash distances
  ☆169Updated last year
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated last week
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆85Updated 2 years ago
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆100Updated 3 years ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆66Updated 2 months ago
• genomehubs / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆104Updated 3 months ago
• ablab / viralVerify
  viralVerify: viral contig verification tool
  ☆71Updated 3 years ago
• fmalmeida / bacannot
  Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
  ☆104Updated 4 months ago
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆174Updated 3 months ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆81Updated 3 months ago
• EBI-Metagenomics / emg-viral-pipeline
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  ☆138Updated last week
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆116Updated last month
• rrwick / Metagenomics-Index-Correction
  ☆83Updated last year
• refresh-bio / kmer-db
  Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, et…
  ☆92Updated 2 months ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆137Updated last year
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆115Updated last year
• genomicsITER / NanoCLUST
  NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  ☆111Updated last year
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆50Updated last year
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated 2 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆59Updated 5 years ago
• genotoul-bioinfo / dgenies
  Dotplot large Genomes in an Interactive, Efficient and Simple way
  ☆107Updated this week
• niemasd / TreeCluster
  Efficient phylogenetic clustering of viral sequences
  ☆88Updated last year
• metagenlab / mummer2circos
  Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments
  ☆107Updated last year