Skip to content

Commit

Permalink
add small runtime example
Browse files Browse the repository at this point in the history
  • Loading branch information
gbouras13 committed Nov 21, 2024
1 parent 20a653a commit 3f6e922
Show file tree
Hide file tree
Showing 2 changed files with 3 additions and 0 deletions.
1 change: 1 addition & 0 deletions HISTORY.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
2. MMSeqs2 is much much faster than BLAST (what took BLAST a few minutes takes MMSeqs2 seconds). We should have written `dnaapler` with `MMseqs2` to begin with.
* The alignment resuls may not be identicial (i.e. they might find specifically different top hits), but the actual reorientation is likely to be identical (at least in my tests). Please reach out or make an issue if you notice any discrepancies.

For example - on my machine (Ubuntu 20.04, Intel i9 13th gen 13900 CPU with 32 threads), for a _Staphylococcus aureus_ genome with 1 small plasmid, `dnaapler -i staph.fasta -o staph_dnaapler -t 8` took ~129 seconds wallclock with `v0.8.1` using `BLAST`, while it took ~3 seconds wallclock with `v1.0.0` using `MMseqs2`.

# 0.8.1 (2024-09-16)

Expand Down
2 changes: 2 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,8 @@ Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recogniti
2. MMSeqs2 is much much faster than BLAST (what took BLAST a few minutes takes MMSeqs2 seconds). We probably should have written `dnaapler` with `MMseqs2` to begin with. `MMSeqs2 v13.45111` was chosen to ensure interoperability with [pharokka](https://github.com/gbouras13/pharokka)
* The alignment resuls may not be identicial to ` dnaapler v0.8.1` (i.e. they might find different top hits), but the actual reorientation is likely to be identical (at least in my tests). Please reach out or make an issue if you notice any discrepancies

For example - on my machine (Ubuntu 20.04, Intel i9 13th gen 13900 CPU with 32 threads), for a _Staphylococcus aureus_ genome with 1 small plasmid, `dnaapler -i staph.fasta -o staph_dnaapler -t 8` took ~129 seconds wallclock with `v0.8.1` using `BLAST`, while it took ~3 seconds wallclock with `v1.0.0` using `MMseqs2`.


# Google Colab Notebooks

Expand Down

0 comments on commit 3f6e922

Please sign in to comment.