diff --git a/HISTORY.md b/HISTORY.md index 7ac491b..11a2299 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -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) diff --git a/README.md b/README.md index 0631fb3..0ea2dcf 100644 --- a/README.md +++ b/README.md @@ -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