Alternatives and similar repositories for nextclade_data

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

• INSaFLU / INSaFLU
  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…
  ☆41Updated this week
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated 3 months ago
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆99Updated 3 years ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated 3 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆103Updated this week
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆49Updated last week
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆88Updated 2 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆98Updated 2 weeks ago
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆60Updated last year
• pianpianyouche / plascad
  Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasm…
  ☆51Updated 5 years ago
• artic-network / primer-schemes
  Primer schemes for real-time genome epidemiology
  ☆30Updated 2 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆73Updated 5 months ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆48Updated 2 months ago
• BigDataBiology / argNorm
  ARG normalization by mapping to the ARO ontology.
  ☆62Updated 6 months ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆71Updated last month
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆43Updated 4 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆81Updated 3 years ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆91Updated 2 months ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆55Updated last year
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 9 months ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆74Updated 2 years ago
• klebgenomics / Kaptive
  ☆57Updated last month
• ksahlin / NGSpeciesID
  Reference-free clustering and consensus forming of long-read amplicon sequencing
  ☆66Updated 9 months ago
• CCB-SB / plsdb
  PLSDB pipeline to collect bacterial plasmids from NCBI
  ☆39Updated last year
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆65Updated last month
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆63Updated 2 weeks ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆51Updated 7 months ago
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆52Updated last year