![]() ![]() We hope you’ll find this resource helpful and beneficial to your research needs. Otherwise, a file path to the blast function must be specified instead. Where “nt.test” is the FASTA sequence of interest and “test.out” is the output file after the search containing the results.Īn important note: When running this function, the FASTA file query must be located inside the bin directory in the SRA Toolkit to use the command format above. For example, if you have a set of run accessions (indicated in the command by ‘ERR’ accession numbers), and you want to search for a particular FASTA sequence, the code would look like the following. The application allows users to compare a FASTA sequence of interest against specific SRA accessions. SRA Toolkit can also be used to run BLAST searches against archived NGS data. Since some of these data files can be exceptionally large, the command-line tools make downloading them that much easier. After applying for access, users can also get restricted-access data from dbGaP, with functions for decrypting and encrypting metadata (for example, phenotype data). The toolkit’s command-line executables allow you to stream data from the NCBI/SRA servers for direct analysis or transform the data into common text formats, such as FASTQ or SAM. ![]() No matter where you download the toolkit from, there are instructions for installation and use as well as an FAQ page. The GitHub web link also provides the uncompiled files for you if you are computer savvy and would like to compile the files yourself. This open-source toolkit can be downloaded from the SRA Toolkit webpage or from GitHub/NCBI and is available for the major operating systems. The SRA Toolkit and GitHub download pages. Data sets can be compared through the SRA web interface, but if you want to integrate these downloads and file conversions into an already existing pipeline, or you simply prefer using a command-line interface, we recommend using the SRA Toolkit.įigure 1. Researchers commonly use SRA data to make discoveries via comparison of data sets. For our purposes here, though, we’re going to assume you already have your files downloaded (and are probably using an implement outside of SRA Toolkit for file i/o) SRA Toolkit is pretty frustrating to use. The Sequence Read Archive (SRA), NCBI’s largest growing repository of molecular data, archives raw sequencing data and alignment information from high-throughput sequencing platforms, including Roche 454 GS Systems®, Illumina’s Genome Analyzer®, and Complete Genomics® systems. If you’re working as an individual or a scientist, you probably want to go ahead and use SRA Toolkit to download your files. ![]()
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