Alternatives and similar repositories for CREST

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

• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆39Updated 9 months ago
• niemasd / ViralConsensus
  Fast viral consensus genome reconstruction
  ☆25Updated 5 months ago
• ansariazim / treeBreaker
  Algorithm to divide a phylogenetic tree into segments based on phenotypes at the leaves of the tree
  ☆25Updated 7 years ago
• gtonkinhill / pairsnp
  A set of scripts for calculating pairwise SNP distance
  ☆43Updated 2 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 6 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 3 months ago
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆16Updated 7 months ago
• zhaoxiaofei / bindash
  Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
  ☆69Updated 4 months ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 6 years ago
• GuyBaele / SpreadGL
  Main development repository for SpreadGL
  ☆20Updated last year
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated 3 weeks ago
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 7 years ago
• nodrogluap / nanostripper
  Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
  ☆14Updated 4 years ago
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆71Updated 5 years ago
• dhelekal / CaveDive
  ☆18Updated last year
• balabanmetin / apples
  distance based phylogenetic placement
  ☆27Updated last year
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• dib-lab / genome-grist
  map Illumina metagenomes to genomes!
  ☆38Updated 2 weeks ago
• FredHutch / FAMLI
  Functional Analysis of Metagenomes by Likelihood Inference
  ☆17Updated 3 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• mbhall88 / streamformatics
  Real-time species-typing visualisation for nanopore data.
  ☆13Updated 2 years ago
• moritzbuck / mOTUlizer
  Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin
  ☆14Updated last year
• tlemane / kmindex
  Index kmtricks bf matrices
  ☆46Updated 2 weeks ago
• geraldinepascal / FROGS
  FROGS is a galaxy/CLI workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data.
  ☆33Updated last month
• prophyle / prophyle
  Accurate, resource-frugal and deterministic DNA sequence classifier.
  ☆36Updated 3 weeks ago
• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆39Updated last year
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• kbseah / genome-bin-tools
  Interactive tools for metagenome visualization and binning in R
  ☆27Updated 7 years ago
• will-rowe / hulk
  Histosketching Using Little Kmers
  ☆56Updated 2 years ago