Home - Green-Biome-Institute/AWS GitHub Wiki

Welcome to the AWS wiki!

Here you will find information on the following:

  1. Using Amazon Web Services for the purpose of genome assembly,
  2. Plant de novo genome assembly using short read, long read, and hybrid short/long read genome assemblers,
  3. Genome assembly QC softwares and metrics,
  4. Comparisons of a variety of genome assemblers,
  5. Tutorials for the command line and implementing genome assembly,
  6. Literature related to plant genetics, de novo genome assembly, assembly in the cloud, and assembly QC!

Tutorials / Trainings:

Informational Content:

Genome Assembly!

Per Assemblathon 2(1), "An assembler may produce an excellent assembly when judged by one approach, but a much poorer assembly when judged by another... Even when an assembler performs well across a range of metrics in one species, it is no guarantee that this assembler will work as well with a different genome... Comparisons between the performance of the same assembler in different species are confounded by the different nature of the input sequence data that was provided for each species." Therefore it is important that we gain experience with multiple different assemblers and find areas they work and benefit each other - this being especially true in plant genomics where there is substantially less information to go off of than other fields of genomics. Here are pages for implementing a variety of different de novo genome assemblers in AWS (Note, there are many more assemblers on the GBI AMI and documentation for them on this github, but to make it simpler, these appear to me the ones we are most likely going to use):

Relevant softwares, papers, and resources


(1) Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. C., Corbeil, J., Fabbro, C. Del, Docking, R. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., … Korf, I. F. (2013). Assemblathon 2: Evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2(1), 1–31. https://doi.org/10.1186/2047-217X-2-10