BOLD BLAST on Hydra walkthrough
- Web BLAST and BOLD ID Engine
Screenshots
- Pros: no setup necessary
- Cons: not very scalable beyond a handful of sequences
- BLAST against NCBI db on Hydra
- Show job file, and stats on resource usage
- Pros: Set it and forget it. Pretty comprehensive, if you want to filter results afterwards.
- Cons: Takes a long time, lots of memory
- BLAST against custom COI db
- Fast enough to show interactively, but also include job file and stats
- Pros: Does have taxonomy included
- Cons: Custom COI db is complicated to build, not all represented
- BLAST against BOLD db
- Fast enough to show interactively, but also include job file and stats
- Pros: Probably more comprehensive than NCBI, since many BOLD records do not get published.
- Cons: Need to link taxonomy as an extra step -- but also pulls in geographic and specimen data.
Next steps
- BLAST alternatives (like https://github.com/bbuchfink/diamond or https://github.com/torognes/vsearch)
- Standardizing database updates
- Non-COI markers