From ce67bc085bf4648f7568bd8b0d908a6581fe1039 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Tue, 1 Oct 2024 09:26:10 +0900 Subject: [PATCH] Update docs/usage.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 60d19da..05860bb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -38,7 +38,7 @@ An [example samplesheet](../assets/samplesheet_full.csv) has been provided with ## Options -The parameters are described in details in the [online documentation](https://nf-co.re/pairgenomealign/parameters). Epert users can pass extra command line arguments to LAST commands. Apart from this the following options are of special importance: +The parameters are described in details in the [online documentation](https://nf-co.re/pairgenomealign/parameters). Expert users can pass extra command line arguments to LAST commands. Apart from this the following options are of special importance: - `--m2m` enables the computation of the _many-to-many_ alignment, which is the only one to be useful in the case of self-alignments, but which on the other hand can exhaust computing resources in the case of very large genomes. - Likewise, when comparing very similar and repetitive genomes (like two vertebrate genomes from the same species), any dotplot other than for the _one-to-one_ alignment will be heavy to compute and useless anyway, because the whole page will be filled with dots. The `--skip_dotplot_*` options are there to solve that problem.