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Background: Read depth is vital in genotyping-by-sequencing and restriction site-based DNA sequencing for polyploids, as well as determining allele dosages. However, new pipelines for GBS and RAD-seq do not include read counts in tables that are both accurate and simple to read. Using user-provided barcodes and tags, the first script, tagdigger_interactive. py, quickly extracts read counts and genotypes from FASTQ files. Barcodesplitter. py is a third script that helps with preparing FASTQ data for deposit in a public archive by splitting FASTQ files by barcode and generating MD5 checksums for the resulting files. TagDigger is an open-source and freely available Python 3 script written in Python 3. TagDigger will run on a laptop with any operating system, does not use much drive space with intermediate files, and does not require programming skills to use.
Source link: https://www.osti.gov/biblio/1629772
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