{"id":239,"date":"2024-10-18T11:07:32","date_gmt":"2024-10-18T09:07:32","guid":{"rendered":"https:\/\/paneec.fr\/?page_id=239"},"modified":"2026-03-25T14:38:45","modified_gmt":"2026-03-25T13:38:45","slug":"production","status":"publish","type":"page","link":"https:\/\/paneec.fr\/index.php\/production\/","title":{"rendered":"Production"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”4.27.2″ _module_preset=”default” background_color=”#1b2838″ global_colors_info=”{}”][et_pb_row _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/12\/Production_LQ2.jpg” alt=”Production | Paneec” title_text=”Production | Paneec” show_bottom_space=”off” align=”center” force_fullwidth=”on” _builder_version=”4.27.2″ _module_preset=”default” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”12px” global_colors_info=”{}”]<\/p>\n

<\/span>Representing a pangenome is always easier in a drawing than in reality (\u00a9 IRD – Eloi Durant)<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”31px” global_colors_info=”{}”]<\/p>\n

PUBLICATIONS<\/strong><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/10\/Zotero.jpg” alt=”Paneec’s publications” title_text=”Zotero” url=”https:\/\/www.zotero.org\/groups\/5530132\/paneec\/collections\/QPJGIPKE” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.2″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

An up-to-date <\/span>list of team members publication is available here<\/a><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.27.2″ _module_preset=”default” min_height=”60px” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”31px” global_colors_info=”{}”]<\/p>\n

TOOLS, PIPELINES, SOFTWARES\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 \u00a0 <\/a>
<\/strong><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” global_colors_info=”{}”]<\/p>\n

Construction, visualisation & manipulation of pangenomes<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/10\/Frangipane.jpg” alt=”FrangiPANe” title_text=”FrangiPANe” url=”https:\/\/github.com\/tranchant\/frangiPANe” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.2″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

<\/span>FrangiPANe<\/strong><\/span><\/a>. Construction of a pangenome reference using the map-then-assembly approach<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/10\/Panache.jpg” alt=”Panache” title_text=”Panache” url=”https:\/\/github.com\/SouthGreenPlatform\/panache” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.2″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

<\/span><\/strong><\/span>Panache<\/strong><\/span><\/a>. Visualisation of linearized pangenomes<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2025\/09\/Savanache.jpg” alt=”Savanache” title_text=”Savanache” url_new_window=”on” show_bottom_space=”off” _builder_version=”4.27.4″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” hover_enabled=”0″ global_colors_info=”{}” sticky_enabled=”0″]<\/p>\n

Savanache<\/strong><\/a>. Visualisation of structural variations in linearized pangenomes pangenomes<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2025\/09\/GraSuite.jpg” alt=”GraSuite” title_text=”GraSuite” url=”https:\/\/forge.ird.fr\/diade\/GraSuite” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.4″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

GraSuite<\/strong><\/a>. A suite of awesome tools for GFA pangenome graph manipulation and pangenome in general<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/10\/Gratools.jpg” alt=”Gratools” title_text=”Gratools” url=”https:\/\/gratools.readthedocs.io\/en\/latest\/” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.2″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

GraTools<\/strong><\/a>. Manipulation of pangenome graphs<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2025\/09\/Temp.jpg” alt=”Temp” title_text=”Temp” url=”https:\/\/forge.ird.fr\/diade\/dynadiv\/grannot” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.4″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

GrAnnoT<\/strong><\/a>. Annotation transfer tool for pangenome graphs<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2025\/09\/Temp.jpg” alt=”Temp” title_text=”Temp” url=”https:\/\/forge.ird.fr\/phim\/gradiv” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.4″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

GraDiv<\/a><\/strong>. \u00a0Diversity analysis on a pangenome graph<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2025\/09\/Temp.jpg” alt=”Temp” title_text=”Temp” url_new_window=”on” show_bottom_space=”off” _builder_version=”4.27.4″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

GraDex<\/strong>. indexation of graph for fast query retrieval<\/p>\n

!! Still under development, not yet public !!<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2025\/09\/Temp.jpg” alt=”Temp” title_text=”Temp” url_new_window=”on” show_bottom_space=”off” _builder_version=”4.27.4″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

GraPheus<\/strong>. A pangenome graph simulator<\/p>\n

!! Still under development, not yet public !!<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2025\/09\/Temp.jpg” alt=”Temp” title_text=”Temp” url_new_window=”on” show_bottom_space=”off” _builder_version=”4.27.4″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” hover_enabled=”0″ global_colors_info=”{}” sticky_enabled=”0″]<\/p>\n

GraNPA<\/strong><\/a>. GWAS using pangenome graph<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” global_colors_info=”{}”]<\/p>\n

Transposable elements<\/span><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/10\/TrEMOLO.jpg” alt=”TReMOLO” title_text=”TrEMOLO” url=”https:\/\/github.com\/DrosophilaGenomeEvolution\/TrEMOLO” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.2″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

<\/span><\/strong><\/span><\/strong><\/span>TrEMOLO<\/strong><\/span><\/a>. Detection of transposable elements using assembly- and mapping-based approaches<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/10\/LTRClassifier.jpg” alt=”LTRClassifier” title_text=”LTRClassifier” url=”https:\/\/ltrclassifier.ird.fr\/LTRclassifier\/form.html” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.2″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

<\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span>LTRclassifier<\/strong><\/span><\/a>. Classification of LTR retrotransposons in plants<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” global_colors_info=”{}”]<\/p>\n

NGS analyses<\/p>\n

\u00a0<\/span><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/10\/CulebrONT.jpg” alt=”CulebrONT” title_text=”CulebrONT” url=”https:\/\/pypi.org\/project\/culebrONT\/” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.2″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

<\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span>CulebrONT<\/strong><\/span><\/a>. Long reads multi-assembler pipeline<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/10\/TOGGLE.jpg” alt=”TOGGLE” title_text=”TOGGLE” url=”https:\/\/github.com\/SouthGreenPlatform\/TOGGLE” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.2″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

<\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span>TOGGLe<\/strong><\/span><\/a>. Building workflows and performing NGS analyses<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”1_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_image src=”https:\/\/paneec.fr\/wp-content\/uploads\/2024\/10\/DuplicationDetector.jpg” alt=”DuplicationDetector” title_text=”DuplicationDetector” url=”https:\/\/github.com\/SouthGreenPlatform\/duplicationDetector” url_new_window=”on” use_overlay=”on” overlay_icon_color=”#51C6F0″ hover_overlay_color=”rgba(81,198,240,0.34)” hover_icon=”||divi||400″ show_bottom_space=”off” _builder_version=”4.27.2″ _module_preset=”default” width=”91.4%” custom_margin=”|16px||||” custom_padding=”|0px||||” border_radii=”on|30px|30px|30px|30px” global_colors_info=”{}”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”4.27.2″ _module_preset=”default” global_colors_info=”{}”][et_pb_text _builder_version=”4.27.2″ _module_preset=”default” text_font_size=”21px” text_line_height=”1.8em” width=”75%” global_colors_info=”{}”]<\/p>\n

<\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span>DuplicationDetector<\/strong><\/span><\/a>. Detection of duplication using NGS data<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

Representing a pangenome is always easier in a drawing than in reality (\u00a9 IRD – Eloi Durant)PUBLICATIONSAn up-to-date list of team members publication is available hereTOOLS, PIPELINES, SOFTWARES\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 \u00a0 Construction, visualisation & manipulation of pangenomesFrangiPANe. Construction of a pangenome reference using the map-then-assembly approachPanache. Visualisation of linearized pangenomesSavanache. Visualisation of structural variations in linearized pangenomes pangenomesGraSuite. A suite of awesome tools for GFA pangenome graph manipulation and pangenome in generalGraTools. Manipulation of pangenome graphsGrAnnoT. Annotation transfer tool for pangenome graphsGraDiv. \u00a0Diversity analysis on a pangenome graphGraDex. indexation of graph for fast query retrieval !! Still under development, not yet public !!GraPheus. A pangenome graph simulator !! Still under development, not yet public !!GraNPA. GWAS using pangenome graphTransposable elementsTrEMOLO. Detection of transposable elements using assembly- and mapping-based approachesLTRclassifier. Classification of LTR retrotransposons in plantsNGS analyses \u00a0CulebrONT. Long reads multi-assembler pipelineTOGGLe. Building workflows and performing NGS analysesDuplicationDetector. Detection of duplication using NGS data<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-239","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/paneec.fr\/index.php\/wp-json\/wp\/v2\/pages\/239","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/paneec.fr\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/paneec.fr\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/paneec.fr\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/paneec.fr\/index.php\/wp-json\/wp\/v2\/comments?post=239"}],"version-history":[{"count":43,"href":"https:\/\/paneec.fr\/index.php\/wp-json\/wp\/v2\/pages\/239\/revisions"}],"predecessor-version":[{"id":789,"href":"https:\/\/paneec.fr\/index.php\/wp-json\/wp\/v2\/pages\/239\/revisions\/789"}],"wp:attachment":[{"href":"https:\/\/paneec.fr\/index.php\/wp-json\/wp\/v2\/media?parent=239"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}