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I posted a similar question in the General Forum a few weeks ago but didn't get any responses. Are there any good libraries for programmatic contig analysis (detecting variations, coverage problems, sequence errors , assembly errors etc). I see that BioJava doesn't have any kind of contig object representation and while BioPerl and BioPython frameworks have contig objects, there doesn't appear to be any built-in analysis methods.
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What kind of sequences do you have - microbial, eukaryote, vertebrate? I have several custom pipelines, plus can guide you to few programs made by others. -
I work with all kinds of data. I have found that lots of people have written custom pipelines that string together a wide variety of tools. Each tool only give a partial answer to the question they want to know. Also many of the tools require different input formats and have their own unique output formats so most of the pipeline is actually only doing format conversion and output parsing.
I was hoping there was a "one stop shop" framework or library that would work for all sizes of genomes that would allow the bio-informatician to programmatically do the specific analysis they wanted.Comment
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The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
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