chromoMapper

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Print all timers (secs) - Monday 02/02/2026 21:58:55 +01:00
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timer                                      secs    secsWait     secsNet   msecsCall      starts       stops    suspends     resumes
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timer                                      0.00        0.00        0.00      0.0010           8           7           0           0
page::output                               0.00        0.00        0.00      0.0012           1           1           1           1
chromoPage::pageContent                    0.00        0.00        0.00      0.4699           1           1           0           0
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ChromoMapper	-	-	-
ChromoMapper is a tool designed to evaluate genome assemblies, starting from the results of a mapping procedure carried out on a reference genome. It quickly identifies and displays similarities and differences between the compared genomes or assemblies using both tables and graphic representations.
About the tool ChromoMapper is optimized for working on alignment results produced by QUAST or other alignment tools to calculate information about alignment blocks together with additional annotations. It represents the main alignment regions at chromosomal or sub-chromosomal scale, highlights similarities and colinearity between the compared sequences, discontinuities and inconsistencies, repeated regions and interruptions in the assembled sequences. It works by integrating mapping data with external info and uses both in a broad range of interactively editable graphical views.
Download ChromoMapper ChromoMapper is available as a command line tool and can be downloaded through Zenodo. It is written in PHP language and does not have any other dependecies.		Documentation	Download
How to reference ChromoMapper has been published in the article: Elvira Toscano, Elena Cimmino, Angelo Boccia, Leandra Sepe, Giovanni Paolella, ChromoMapper: a new tool to quickly compare large genome assemblies, Bioinformatics Advances, 2026; vbag005, https://doi.org/10.1093/bioadv/vbag005 The article provides further details about design, implementation and utilization of the program.			Download PDF
Contact Giovanni Paolella (giovanni.paolella@unina.it)

ChromoMapper 1.5.7

CEINGE-Biotecnologie Avanzate Franco Salvatore

Università degli Studi di Napoli Federico II