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
  ☆129Updated last year
• lskatz / mashtree
  Create a tree using Mash distances
  ☆177Updated 2 years ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated last week
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆145Updated this week
• khyox / recentrifuge
  Recentrifuge: robust comparative analysis and contamination removal for metagenomics
  ☆99Updated 7 months ago
• EBI-Metagenomics / emg-viral-pipeline
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  ☆144Updated 3 weeks ago
• niemasd / TreeCluster
  Efficient phylogenetic clustering of viral sequences
  ☆89Updated 3 weeks ago
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆85Updated 2 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆117Updated last year
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆180Updated 7 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆121Updated last week
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆52Updated last year
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆106Updated 4 years ago
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆97Updated 2 weeks ago
• ablab / viralVerify
  viralVerify: viral contig verification tool
  ☆72Updated 4 years ago
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆142Updated 2 years ago
• fmalmeida / bacannot
  Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
  ☆104Updated 2 weeks ago
• genomicsITER / NanoCLUST
  NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  ☆113Updated 2 years ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆83Updated 3 months 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
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆66Updated 2 years ago
• genomehubs / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆116Updated this week
• snayfach / MIDAS
  An integrated pipeline for estimating strain-level genomic variation from metagenomic data
  ☆131Updated 2 years 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
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆124Updated 2 years ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆75Updated last year
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆75Updated 2 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆81Updated 3 years ago