From 20a653a6934b6ef5373ef2ea66ba0ad6ddbe9139 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Thu, 21 Nov 2024 10:11:31 +1030 Subject: [PATCH] update readme again --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 32b599a..0631fb3 100644 --- a/README.md +++ b/README.md @@ -61,7 +61,7 @@ Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recogniti ## v1.0.0 -* **BREAKING CHANGE** - `dnaapler` now uses `MMSeqs2 v13.45111` rather than `BLAST`. You will need to install [MMSeqs2](https://github.com/soedinglab/MMseqs2) if you upgrade (if you use conda, it should be handled for you) +* **BREAKING CHANGE** - `dnaapler` now uses `MMSeqs2 v13.45111` rather than `BLAST`. You will need to install [MMSeqs2](https://github.com/soedinglab/MMseqs2) if you upgrade (if you use conda, it should be handled for you). The CLI is identical. * There are 2 reasons for this: 1. Users reported problems installing BLAST on MacOS with Apple Silicon (see e.g. [here](https://github.com/gbouras13/pharokka/issues/368)). MMseqs2 works on all platforms and is dilligently maintained. 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) @@ -130,9 +130,9 @@ The full documentation for `dnaapler` can be found [here](https://dnaapler.readt ## Installation -`dnaapler` requires only BLAST v2.10 or higher as an external dependency. +`dnaapler` requires only `MMseqs2 v13.45111` as an external dependency. -Installation from conda is highly recommended as this will install BLAST automatically. +Installation from conda is highly recommended as this will install `MMseqs2` automatically. ### Conda @@ -150,7 +150,7 @@ You can also install `dnaapler` with pip. pip install dnaapler ``` -* If you install `dnaapler` with pip, then you will then need to install BLAST v 2.9 or higher separately. It will need to be available in the `$PATH` or else `dnaapler` will not work. +* If you install `dnaapler` with pip, then you will then need to install `MMseqs2 v13.45111` separately. It will need to be available in the `$PATH` or else `dnaapler` will not work. ## Usage @@ -186,14 +186,14 @@ Options: -V, --version Show the version and exit. -i, --input PATH Path to input file in FASTA format [required] -o, --output PATH Output directory [default: output.dnaapler] - -t, --threads INTEGER Number of threads to use with BLAST [default: 1] + -t, --threads INTEGER Number of threads to use with MMseqs2 [default: 1] -p, --prefix TEXT Prefix for output files [default: dnaapler] -f, --force Force overwrites the output directory -e, --evalue TEXT e value for MMseqs2 [default: 1e-10] --ignore PATH Text file listing contigs (one per row) that are to be ignored -a, --autocomplete TEXT Choose an option to autocomplete reorientation if - BLAST based approach fails. Must be one of: none, + MMseqs2 based approach fails. Must be one of: none, mystery, largest, or nearest [default: none] --seed_value INTEGER Random seed to ensure reproducibility. [default: 13] @@ -260,7 +260,7 @@ dnaapler bulk -i input_file_with_multiple_chromosomes.fasta -m chromosome -o out `dnaapler custom` uses a custom amino acid FASTA format file that you specify using `-c`. -The matching is strict - it requires a strong BLASTx match (default e-value 1E-10), and the first amino acid of a BLASTx hit gene to be identified as Methionine, Valine or Leucine, the 3 most used start codons in bacteria/phages. +The matching is strict - it requires a strong MMseqs2 match (default e-value 1E-10), and the first amino acid of a MMseqs2 hit gene to be identified as Methionine, Valine or Leucine, the 3 most used start codons in bacteria/phages. For the most commonly studied microbes (ESKAPE pathogens, etc), the dnaA database should suffice.