Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with `-e`), and a pan-genome reference. Use Panaroo for higher-accuracy pan-genomes from highly fragmented assemblies, PIRATE for paralog-aware clustering, or PPanGG
Receba novas skills de DevOps e Infra toda segunda
1 email curto, só com as skills novas de DevOps e Infra. 4 minutos de leitura, sem spam, cancela com 1 clique.
Você confirma o email no primeiro envio. Sem spam. Cancela com 1 clique.
Ler descrição completaRecolher descrição
Roary Pan-Genome Pipeline
Overview
Roary is a high-throughput pan-genome pipeline for prokaryotes that takes per-sample GFF3 annotations (typically from Prokka or Bakta) and produces a clustered gene presence/absence matrix across the entire input set. It first reduces redundancy with CD-HIT iterative clustering, then performs an all-vs-all BLASTP within each pre-cluster, and finally applies MCL graph clustering to define orthologous gene families. The output partitions the gene space int
[Description truncada. Veja o README completo no GitHub.]
