Alternatives and similar repositories for strain_phylogenetics:

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

• colindaven / guppy_on_slurm
  Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler
  ☆15Updated 6 months ago
• m-crown / SPEAR
  Systematic ProtEin AnnotatoR
  ☆19Updated 3 months ago
• niemasd / ViralConsensus
  Fast viral consensus genome reconstruction
  ☆22Updated last month
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆15Updated last year
• fbreitwieser / card-krakendb
  Scripts for creating a Kraken database from the Comprehensive Antibiotic Resistance Database
  ☆10Updated 8 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆24Updated last year
• broadinstitute / delphy
  Fast, scalable, accurate and accessible Bayesian phylogenetics
  ☆29Updated this week
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆31Updated 2 months ago
• dhelekal / CaveDive
  ☆17Updated 7 months ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆34Updated last week
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆32Updated last month
• bede / kindel
  Indel-aware consensus for aligned BAM
  ☆21Updated last month
• amkram / shusher
  Private, browser-based placement of genome sequences on phylogenetic trees using UShER.
  ☆10Updated 2 months ago
• ansariazim / treeBreaker
  Algorithm to divide a phylogenetic tree into segments based on phenotypes at the leaves of the tree
  ☆25Updated 6 years ago
• beardymcjohnface / Koverage
  Quickly get coverage statistics given reads and an assembly
  ☆13Updated 8 months ago
• asmngs / asmngs20
  ASMNGS20 - 2020 Conference Details
  ☆15Updated 2 years ago
• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆22Updated 9 months ago
• iqbal-lab-org / varifier
  Variant call verification
  ☆15Updated 2 weeks ago
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆27Updated last month
• chrisquince / StrainMetaSim
  Strain resolved metagenome simulator
  ☆13Updated 6 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• kwongj / cfml-maskrc
  Masks recombinant regions in an alignment based on ClonalFrameML output
  ☆10Updated 6 years ago
• jmcbroome / autolin
  Repository containing a method for automatically identifying pathogen lineages from a phylogeny.
  ☆14Updated last year
• PROBIC / mGEMS
  mGEMS Genomic epidemiology with mixed samples
  ☆16Updated 4 months ago
• sdwfrost / gbmunge
  Munge GenBank files into FASTA and tab-separated metadata
  ☆14Updated last year
• LuoGroup2023 / PanTax
  Strain-level taxonomic classification of metagenomic data using pangenome graphs
  ☆22Updated 2 months ago
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated last month
• c2-d2 / disty
  Disty McMatrixface - compute a distance matrix from a core genome alignment file
  ☆14Updated last year
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated last week