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• pipelines for pan-genome analysis
  I have bacterial genome and  which pipeline is best  for pan-genome analysis ? 
• BPGA - Bacterial Pan Genome Analysis pipeline
  BPGA is a fast pan-genome analysis tool for microbial genomes. Along with regular pan genome prof...
• pancoreplot CMG-Biotools, file plot
  hi, I have made a pan genome analysis of 6 genomes, the pipeline that I used was: generate a th...
• BPGA - how to update KEGG and COG database?
  I am using BPGA tool for pan genome analysis. It uses COG and KEGG database to find significant f...
• BPGA Functional Analysis not working
  Hi, I have been using BPGA (Bacterial Pan Genome Analysis) to analyze a set of genomes in order t...
• Noisy germline CNV data using CNVKit
  **Context:** I'm a new CNVKit user (using 0.9.6). I have 6 exome-seq samples (from saliva DNA) th...
• Problem while using BPGA-Version-1.3 for pan bacterial genome analysis
  I am trying to find similar and non-similar genes by analyzing whole genomes of 147 strains. I am...
• Is it advisable to include reference genome for pan-genome anlysis when working on specific type strains?
  I constructed and analyzed pan-genome but now I got this doubt: Is it advisable to include refere...
• One gene shows alignment with core sequences as well as with accessory gene sequences at 50% identity?
  Hi I have done pan-genome analysis with 0.5% identity cutoff using BPGA tool. and it has given me...
• Query about PID in .ptt file
  Hi Biostars Community, I am doing pangenome analysis on Pan-X pipeline. I tried to used it onlin...
• What is the minimum number/threshold of gaps (NNNNNN) permitted in a draft genome?
  I did a bacterial whole genome sequencing by illumina platform. The quality raw reads were subjec...
• Pan Genome Claculation using PanGP
            Hi Guys, Does anyone have experience about  PanGP to plot Pan genome and core gen...
• Pan genome analysis tool (PGAP)
  Hi, After searching on internet I found this Tools called PGAP which comes under the top two Pa...
• error while executing panX script (KeyError: 'db_xref').
  I have been working with [panX][1]. I ran the test dataset without any error. But, while running ...
• Why is there no pipeline (windows based) for pangenome analysis of eukaryotes?
  EUPAN is a pipeline I came across which basically just lists down all linux based softwares to be...
• Annotating Core and Pan genome
  Hello, I have used get_homologues pipeline to predict core and pan genome among a group of bacte...
• How to increase point size or color palette of a PCA plot using the scater package for scRNA analysis
  Hi, I am using scater to analyze my single cell data. However the plotPCA function has a fixed p...
• Pan- and core- genome in bacteria
  Hi, I want to find pan genome in bacteria, which include subsequent analysis of core, dispensabl...