Here’s a brief overview of what Sean has done with the Oly genome assembly front.
- Assemble his BGI assembly and Platanus assembly? Confusing terms here; not sure what he means.
- Failed due to 32-bit vs. 64-bit installation of MUMmer. He didn’t have the chance to re-compile MUMmer as 64-bit. However, a recent MUMmer announcement suggests that MUMmer can now handle genomes of unlimited size.
- I believe he was planning on using (or was using?) GARM, which relies upon MUMmer and may also include a version of MUMmer (outdated version that led to Sean’s error message?).
- Notebook entry
- Assemble UW PacBio data (filenames beginning with m170211, m170315, m170308, and m170301).
- Files (including Mox scripts, Pilon contig polishing, & output FASTA files) are here: http://ift.tt/2iDHekA
- Notebook entry
- Assembled raw Illumina reads provided by BGI (filenames beginning with 15114 and 16103) & UW PacBio data (filenames beginning with m170211, m170315, m170308, and m170301).
- Ran this two times.
- First run
- Files (including Mox scripts & output FASTA files) are here: http://ift.tt/2qWWRWK
- Notebook entry
- Second run
- Files (including Mox scripts & output FASTA files) are here: http://ift.tt/2s8mOUD
- Notebook entry
- Assembled raw Illumina reads provided by BGI (beginning with 15114 and 16103).
- Ran this two times.
- First run
- Files (including Mox scripts & output FASTA files) are here: http://ift.tt/2q1vS9a
- Notebook entry
- Second run
- Files (including Mox scripts & output FASTA files) are here: http://ift.tt/2iDHgJe
- Notebook entry
from Sam’s Notebook http://ift.tt/2iDa9VQ
Project Progress – Olympia Oyster Genome Assemblies by Sean Bennett