Alternatives and similar repositories for usher

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

• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆114Updated 11 months 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 last year
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆55Updated 8 months ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆158Updated this week
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆135Updated last year
• artic-network / fieldbioinformatics
  The ARTIC field bioinformatics pipeline
  ☆122Updated last week
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆83Updated 2 years ago
• andersen-lab / Freyja
  Depth-weighted De-Mixing
  ☆114Updated this week
• andersen-lab / ivar
  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
  ☆120Updated this week
• BenoitMorel / GeneRax
  ☆70Updated last year
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆97Updated 2 years ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆73Updated last year
• nickjcroucher / gubbins
  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
  ☆190Updated last month
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆115Updated 2 months ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆78Updated 8 months ago
• artic-network / artic-ncov2019
  ARTIC nanopore protocol for nCoV2019 novel coronavirus
  ☆170Updated 2 years ago
• neherlab / treetime
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
  ☆241Updated last month
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆126Updated this week
• marbl / parsnp
  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…
  ☆140Updated 2 weeks ago
• asl / BandageNG
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆129Updated 2 weeks ago
• replikation / What_the_Phage
  WtP: Phage identification via nextflow and docker or singularity
  ☆105Updated this week
• lskatz / mashtree
  Create a tree using Mash distances
  ☆164Updated last year
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆83Updated this week
• ddarriba / modeltest
  Best-fit model selection
  ☆81Updated last year
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆85Updated 3 months ago
• neherlab / pangraph
  A bioinformatic toolkit to align genome assemblies into pangenome graphs
  ☆103Updated last month
• jts / ncov-tools
  Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  ☆48Updated last year
• phac-nml / mob-suite
  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  ☆146Updated last month
• roblanf / sarscov2phylo
  Global phylogenies of SARS-CoV-2 sequences
  ☆86Updated last year
• rrwick / Polypolish
  a short-read polishing tool for long-read assemblies
  ☆159Updated 11 months ago