From 59c841bd23389aa14392b2bcb4bed66b79a2dd80 Mon Sep 17 00:00:00 2001 From: Alexis CRISCUOLO <alexis.criscuolo@pasteur.fr> Date: Wed, 9 Mar 2022 09:13:48 +0100 Subject: [PATCH] 1.3 --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index c471acf..56e1463 100644 --- a/README.md +++ b/README.md @@ -69,21 +69,21 @@ Run _GenoLayout_ without option to read the following documentation: ## Notes -* In brief, for each pair of genomes, _GenoLayout_ decomposes each of them into overlapping fragments. Fragment length is set by option `-w` (default: 1000). Each set of fragments is searched against the other using blastn (Altschul et al. 1990; Camacho et al. 2008) with tuned parameters (as suggested by Goris et al. 2007). Orthologous fragments are assessed by reciprocal BLAST hits showing ≥ 30 % overall fragment identity on an alignable region ≥ 35% fragment lengths (as suggested by Lee et al. 2016). Each genome is graphically represented by a box (of length proportional to the overall genome length), and each pair of orthologous fragments is represented by a line. +* In brief, for each pair of genomes, _GenoLayout_ decomposes each of them into overlapping fragments. Fragment length is set by option `-w` (default: 1000). Each set of fragments is searched against the other using blastn (Altschul et al. 1990; Camacho et al. 2008) with tuned parameters (as suggested by Goris et al. 2007). Orthologous fragments are assessed by reciprocal BLAST hits showing ≥ 30 % overall fragment identity on an alignable region ≥ 35% fragment lengths (as suggested by Lee et al. 2016). Each genome is graphically represented by a box, and each pair of orthologous fragments is represented by a line. * Each input file should be in FASTA format, not compressed, and may contain nucleotide sequences. At least two input files should be specified. If more than two files are specified, the file order is followed to draw the pairwise linear maps. -* Faster running times can be obtained in three ways: (i) by using large BLAST _k_-mer lengths (option `-k`; default: 35), but at the cost of a reduced accuracy; (ii) by using larger fragment lengths (option `-w`; default: 1000), but at the cost of a reduced number of orthologous fragment pairs; (iii) by using a large number of threads (option `-t`). +* Faster running times can be obtained in three ways: (i) by using large BLAST _k_-mer lengths (option `-k`; default: 25), but at the cost of a reduced accuracy; (ii) by using larger fragment lengths (option `-w`; default: 1000), but at the cost of a reduced number of orthologous fragment pairs; (iii) by using a large number of threads (option `-t`; default: 2; recommended: 12). * For distantly-related genomes (e.g. expected average nucleotide identity ≤ 80%), it is recommended to use short _k_-mers for BLAST searches (e.g. `-k 11`). -* Figure width is automatically determined from both the maximum genome length _lmax_ and the fragment length _w_ (option `-w`). However, a span factor _s_ (option `-s`; default: 1.0) can be used to increase (_s_ \> 1.0) or decrease (_s_ < 1.0) the figure width. The overall figure width (in px) is: 100 + 2 _lmax_ × _s_ ∕ _w_. Of note, a final scale factor of 0.1 is applied to the overall figure dimensions. +* Figure width is automatically determined from both the maximum genome length _g_ and the fragment length _w_ (option `-w`). However, a span factor _s_ (option `-s`; default: 1.0) can be used to increase (_s_ \> 1.0) or decrease (_s_ < 1.0) the figure width. The overall figure width (in px) is: 100 + 2 _g_ × _s_ ∕ _w_. Of note, a final scale factor of 0.1 is applied to the overall figure dimensions. -* Figure height can be controlled using options `-x` (genome box height, in px) and `-y` (gap height between boxes where the lines are drawn, in px). Default values (in px) are _x_ = 0.1 _lmax_ ∕ _w_, _y_ = 5 _x_ and _z_ = 0.75 _x_, respectively. When inputing _n_ files, the overall figure height (in px) is: 100 + _n_ _x_ + (_n_ − 1) _y_. Of note, a final scale factor of 0.1 is applied to the overall figure dimensions. +* Figure height can be controlled using options `-x` (genome box height, in px) and `-y` (gap height between boxes where the lines are drawn, in px). Default values (in px) are _x_ = 0.1 _g_ ∕ _w_, _y_ = 5 _x_ and _z_ = 0.75 _x_, respectively. When inputing _n_ files, the overall figure height (in px) is: 100 + _n_ _x_ + (_n_ − 1) _y_. Of note, a final scale factor of 0.1 is applied to the overall figure dimensions. * Font (i.e. file names), box (i.e. genome) and line (i.e. orthologous fragments) colors can be modified using options `-a`, `-b` and `-c`, respectively. Color names should correspond to the [SVG specification](https://www.december.com/html/spec/colorsvg.html). -* To reduce the size of the output file (and sometimes obtain a better reading), it is also possible to draw a periodic subset of lines between genome boxes using option `-j`. For example, setting `-j 2` draws only half lines (i.e. one every two) and enables to divide the file size by two, without significantly altering the final render. Of note, as some conversion tools can lead to thicker lines (e.g. [_Inkscape_](https://inkscape.org/), [_rsvg-convert_](https://gitlab.gnome.org/GNOME/librsvg)), setting option `-j` with a somewhat large value (e.g. `-j 9`) can help obtaining clearer figures in e.g. pdf or png format. +* To reduce the size of the output file (and sometimes obtain a better reading), it is possible to draw a periodic subset of lines between genome boxes using option `-j`. For example, setting `-j 2` draws only half lines (i.e. one every two) and enables to divide the file size by two, without significantly altering the final render. Of note, as some conversion tools can lead to thicker lines (e.g. [_Inkscape_](https://inkscape.org/), [_rsvg-convert_](https://gitlab.gnome.org/GNOME/librsvg)), setting option `-j` with a somewhat large value (e.g. `-j 9`) can help obtaining clearer figures in e.g. [PDF](https://www.adobe.com/acrobat/about-adobe-pdf.html) or [PNG](https://www.w3.org/TR/PNG/) format. ## Examples @@ -177,7 +177,7 @@ GenoLayout.sh -t 48 -w 500 -j 2 -x 50 -y 4000 -z 0 -b black -c darkorange • Converting SVG files -[_Inkscape_](https://inkscape.org/) can be used to convert SVG files into e.g. PDF of PNG files: +[_Inkscape_](https://inkscape.org/) can be used to convert SVG files into e.g. [PDF](https://www.adobe.com/acrobat/about-adobe-pdf.html) or [PNG](https://www.w3.org/TR/PNG/) files: ```bash inkscape --export-png=genolayout.png genolayout.svg -- GitLab