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pachterlab / metakallisto

Using kallisto for metagenomic analysis
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Metakallisto documentation #1

Open jacodela opened 5 years ago

jacodela commented 5 years ago

Hello, I want to use Metakallisto to determine the abundance of multiple genomes from a clade in different metagenomic samples. However, I find the documentation lacking, and I have several questions:

  1. How can I generate a custom genome database to be used with Metakalisto?
  2. Should Mash be run on the metagenomes, the database of genomes or both?
  3. Should Mash be run independently prior running the Metakalisto scripts or does the mash_kallisto_pipeline.py script run it?
  4. I don't quite understand the top_strains parameter in the mash_kallisto_pipeline.py. Could you clarify it?
  5. Can you provide a working example of how the scripts should be executed?

Thanks!

anuradhawick commented 4 years ago

I am planning to run some binning analysis using Metakallisto. Is it possible to use DNA contigs (resulted from assembly)? Please provide a complete example starting with FASTA sequences (or whatever the input shall be). Documentation is unclear. Thank you