Do you work with human-derived sequence data? Do you often struggle with the need to determine if your data is free of human sequence and therefore suitable for public distribution? We encourage submitters to screen for and remove contaminating human reads from data files prior to submission to SRA. To support investigators in this effort, we offer a tool to remove human sequence contamination from your SRA submissions!
Human Read Removal Tool (HRRT)
The Human Read Removal Tool (HRRT; also known as the Human Scrubber) is available on GitHub and DockerHub. The HRRT is based on the SRA Taxonomy Analysis Tool (STAT) that will take as input a fastq file and produce as output a fastq.clean file in which all reads identified as potentially of human origin are masked with ‘N’. Continue reading “Scrubbing human sequence contamination from Sequence Read Archive (SRA) submissions”
RefSeq release 216 is now available online, from the FTP site, and through NCBI’s new resource, Datasets.
This full release incorporates genomic, transcript, and protein data available as of January 9, 2023, and contains 342,395,932 records, including 249,868,639 proteins, 49,869,497 RNAs, and sequences from 128,299 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 216” →