Productive visualization of high-throughput sequencing data using the SeqCode open portable platform

Large-scale sequencing techniques to chart genomes are entirely consolidated. Stable computational methods to perform primary tasks such as quality control, read mapping, peak calling, and counting are likewise available. However, there is a lack of uniform standards for graphical data mining, which is also of central importance. To fill this gap, we developed SeqCode, an open suite of applications that analyzes sequencing data in an elegant but efficient manner. Our software is a portable resource written in ANSI C that can be expected to work for almost all genomes in any computational configuration. Furthermore, we offer a user-friendly front-end web server that integrates SeqCode functions with other graphical analysis tools. Our analysis and visualization toolkit represents a significant improvement in terms of performance and usability as compare to other existing programs. Thus, SeqCode has the potential to become a key multipurpose instrument for high-throughput professional analysis; further, it provides an extremely useful open educational platform for the world-wide scientific community. SeqCode website is hosted at http://ldicrocelab.crg.eu , and the source code is freely distributed at https://github.com/eblancoga/seqcode.The work in the Di Croce laboratory is supported by grants from the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) (PID2019-108322 GB-I00), Fundación Vencer El Cancer (VEC), and the Catalan Agency for Management of University and Research Grants (AGAUR). We acknowledge support from the Spanish Ministry of Science and Innovation to the EMBL partnership Centro de Excelencia Severo Ochoa, and the CERCA Programme/Generalitat de Cataluny