Software on Maragkakis Labhttp://maragkakislab.com/tags/software/Recent content in Software on Maragkakis LabHugoen-usSat, 02 Oct 2021 00:00:00 +0000SamQL: A Structured Query Language and filtering tool for the SAM/BAM file formathttp://maragkakislab.com/publications/2021-samql/Sat, 02 Oct 2021 00:00:00 +0000http://maragkakislab.com/publications/2021-samql/<h2 id="summary">Summary</h2> <p>SamQL implements a SQL-like query language for filtering and extracting reads from SAM/BAM alignment files based on arbitrary combinations of alignment attributes. The tool enables complex queries that are not possible with existing SAM/BAM filtering utilities, facilitating flexible downstream analysis of sequencing data.</p>bíogo: a simple high-performance bioinformatics toolkit for the Go languagehttp://maragkakislab.com/publications/2017-biogo/Sat, 18 Feb 2017 00:00:00 +0000http://maragkakislab.com/publications/2017-biogo/<h2 id="summary">Summary</h2> <p>bíogo is a bioinformatics library written in the Go programming language, providing high-performance tools for common genomic data processing tasks. The toolkit offers a clean API for sequence manipulation, alignment, and genomic data parsing with the performance characteristics of a compiled language.</p>CLIPSeqTools — a novel bioinformatics CLIP-seq analysis suitehttp://maragkakislab.com/publications/2016-clipseqtools/Fri, 01 Jan 2016 00:00:00 +0000http://maragkakislab.com/publications/2016-clipseqtools/<h2 id="summary">Summary</h2> <p>CLIPSeqTools is a modular bioinformatics pipeline for the analysis of CLIP-seq data, providing tools for read processing, peak calling, motif analysis, and visualization. The suite enables comprehensive characterization of RNA-binding protein interaction sites across the transcriptome.</p>