6 papers · ranked by Valyu relevance
Tycho Kirchner, Konstantin Riege, Steve Hoffmann
Arguably, the most important tool for many computational scientists is the Linux shell. Processing steps carried out there are critical for a large number of analyses. While the manual documentation of the work is time-consuming and error-prone, existing tools do not integrate well into the shell or suffer from a large…
Daniel Ortiz-Martínez
Background Bioinformatics data analysis faces significant challenges. As data analysis often takes the form of pipelines or workflows, workflow managers (WfMs) have become essential. Data flow programming constitutes the preferred approach in WfMs, enabling parallel processes activated reactively based on input…
Nathan Edwards, Christian Dillard, N M Prashant, Liu Hongyu + 4 more
SCExecute is modeled after the classic Linux tools find and xargs, which execute a command repeatedly on a collection of files. Instead of generating scBAMs for all cellular barcodes first, and only then executing a command on each scBAM, SCExecute interleaves the generation of a batch of scBAMs and execution of the…
Florian Rupprecht, Jason Kai, Biraj Shrestha, Steven Giavasis + 4 more
'Ting Xu' 'Tristan Glatard' 'Michael P Milham' 'Gregory Kiar'] In numerous scientific domains, established tools have often been developed with complex command-line interfaces. Such is the case for brain imaging and bioinformatics, making the use of powerful legacy tools in modern workflow paradigms challenging. We…
Xinwei Zhao, Eberhard Korsching, Philip Hublitz
DNA and RNA nucleotide sequences are ubiquitous in all biological cells, serving as both a comprehensive library of capabilities for the cells and as an impressive regulatory system to control cellular function. The multi-alignment framework (MAF) provided in this study offers a user-friendly platform for sequence…
Wei Shen, Botond Sipos, Liuyang Zhao
In the era of ubiquitous high-throughput sequencing studies, there is a growing need for analysis tools that are not just performant but also comprehensive and user-friendly enough to cater to both novice and advanced users. This article introduces SeqKit2, the next iteration of the widely used sequence analysis tool…