Alternatives and similar repositories for lineages

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

• kdm9 / kWIP
  De novo estimates of genetic relatedness from next-gen sequencing data
  ☆45Updated 6 years ago
• cov-lineages / llama
  Local Lineage and Monophyly Assessment
  ☆16Updated 4 years ago
• edawson / rkmh
  Classify sequencing reads using MinHash.
  ☆48Updated 5 years ago
• maximilianh / multiSub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆36Updated 3 years ago
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆28Updated 3 weeks ago
• dkoslicki / MetaPalette
  Metagenomic profiling and phylogenetic distances via common kmers
  ☆42Updated 4 years ago
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated 3 months ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated last month
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 6 years ago
• GuyBaele / SpreadGL
  Main development repository for SpreadGL
  ☆19Updated last year
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• janepipistrelle / bacterial_GWAS_tutorial
  Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
  ☆18Updated 9 years ago
• WGS-standards-and-analysis / datasets
  Benchmark datasets for WGS analysis
  ☆39Updated 6 years ago
• cov-lineages / scorpio
  serious constellations of reoccurring phylogenetically-independent origin
  ☆39Updated 2 years ago
• sanger-pathogens / pymummer
  Python3 module for running MUMmer and reading the output
  ☆33Updated 6 months ago
• jaleezyy / covid-19-signal
  Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
  ☆31Updated last month
• niemasd / ViralMSA
  Reference-guided multiple sequence alignment of viral genomes
  ☆70Updated 4 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
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆16Updated 5 months ago
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆23Updated 3 weeks ago
• ukhsa-collaboration / variant_definitions
  ☆74Updated last year
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago
• onecodex / sars-cov-2
  SARS-CoV-2 variant calling and consensus assembly pipeline
  ☆25Updated 2 years ago
• bcthomas / pullseq
  Utility program for extracting sequences from a fasta/fastq file
  ☆35Updated 9 months ago
• iqbal-lab / Mykrobe-predictor
  Antibiotic resistance predictions in minutes on a laptop
  ☆50Updated 6 years ago
• geraldinepascal / FROGS
  FROGS is a galaxy/CLI workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data.
  ☆31Updated 2 weeks ago
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated 3 weeks ago
• m-crown / SPEAR
  Systematic ProtEin AnnotatoR
  ☆19Updated 3 weeks ago
• snayfach / IGGsearch
  Metagenomic species profiling with enhanced coverage of the human gut microbiome
  ☆24Updated last year
• ukhsa-collaboration / PHEnix
  Public Health England SNP calling pipeline.
  ☆37Updated 7 years ago