Alternatives and similar repositories for phoenix

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

• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆98Updated 2 months ago
• theiagen / public_health_viral_genomics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…
  ☆41Updated 10 months ago
• nf-core / readsimulator
  A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
  ☆31Updated this week
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆55Updated 9 months ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆86Updated 3 months ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆51Updated last month
• CDCgov / mycosnp-nf
  MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates
  ☆65Updated 2 weeks ago
• shandley / hecatomb
  hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
  ☆57Updated 2 weeks ago
• jodyphelan / tbdb
  Standard database for the TBProfiler tool
  ☆29Updated 2 months ago
• ncbi / rapt
  This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
  ☆57Updated 2 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 2 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆43Updated 2 months ago
• voorloopnul / awesome-phages
  A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
  ☆48Updated 2 years ago
• wslh-bio / spriggan
  Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.
  ☆16Updated this week
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated last month
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated 8 months ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆74Updated last year
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆40Updated 6 months ago
• BigDataBiology / argNorm
  ARG normalization by mapping to the ARO ontology.
  ☆57Updated last month
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 11 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated last year
• dbeisser / Natrix2
  Natrix2 is an open-source bioinformatics pipeline for preprocessing raw amplicon sequencing and metabarcoding data.
  ☆12Updated last week
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆59Updated 9 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• fmalmeida / bacannot
  Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
  ☆103Updated 2 months ago
• richardmleggett / MARTi
  Metagenomic Analysis in Real Time
  ☆24Updated last week
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆79Updated last month