Fastq file download

The SRA runs e. SRR correspond to the actual sequencing files that we want to download in order to access the raw data. This means that the lab had deposited multiple FASTQ files for one sample and did not bother to concatenate them together prior to deposition.

You can get more details about how each sample was prepared clicking on the GSM identifier in the Samples section from the first image e. This will take you to the sample description page. I have summarized the different identifiers for GSE in the following table:. But what is a. If you are using a Linux platform, you can type: apt install sra-toolkit in your command line to install the toolkit.

The file SRR Could not load branches. Could not load tags. Latest commit. Git stats commits. Failed to load latest commit information. View code. Kingfisher Installation Usage 'get' mode: Download and optionally convert sequence data 'extract' mode: Convert sequence data from. Installation Kingfisher can be installed by installing its conda dependencies as follows. Topics sra aspera-client fastq-files.

Releases No releases published. Packages 0 No packages published. Our variant files are distributed in vcf format , a format initially designed for the Genomes Project which has seen wider community adoption. This name starts with the population that the variants were discovered in, if ALL is specifed it means all the individuals available at that date were used.

Then the region covered by the call set, this can be a chromosome, wgs which means the file contains at least all the autosomes or wex this represents the whole exome and a description of how the call set was produced or who produced it, the date matches the sequence and alignment freezes used to generate the variant call set. Next a field which describes what type of variant the file contains, then the analysis group used to generate the variant calls, this should be low coverage, exome or integrated and finally we have either sites or genotypes.

A sites file just contains the first eight columns of the vcf format and the genotypes files contain individual genotype data as well. Release directories should also contain panel files which also describe what individuals the variants have genotypes for and what populations those individuals are from. Format We use Sanger style phred scaled quality encoding. The files are all gzipped compressed and the format looks like this, with a four-line repeating pattern ERR Edit: see also the many alternatives posted as followups.

I am cleaning the cache in my examples only to ensure that I correctly measure the performance. Total time 5 minutes. On my system is located in. Subsequent fastq dump on the same accession will take 1 minute. The principal advantage of fastq-dump over all other methods is that it supports the partial download of data. According to the documentation, it requires up to 10x as much disk space as the final file.

In addition, it does not yet support downloading a subset of the data as fastq-dump does:. The challenge here is to find the proper URLs. The sratools prefetch command will download an SRA then store it in a cache directory.