Data¶

The exercises use the datasets below. The easiest way to get them is to import the shared Galaxy history for the exercise. It already contains every file with the correct datatype.

If you download the files yourself, upload them to Galaxy with the datatype listed in the table. You can check that a download is complete by comparing its SHA-256 checksum with the one listed here.

Datasets¶

NGS preprocessing and quality control¶

Used in the exercise NGS preprocessing and quality control.

How to get the data

Recommended: import the shared Galaxy history: https://usegalaxy.eu/u/bentpetersen/h/kp-preprocessing-data. It already contains every file with the correct datatype, and the paired collection.
Direct download of the individual files: links in the table below. Upload them to Galaxy with the datatype shown.

File	Description	Technology	Layout	Galaxy datatype	Size
`Paeruginosa.fastq.gz`	Pseudomonas aeruginosa, clinical isolate from a Danish transmissible lineage	Illumina	single-end	`fastqsanger.gz`	73 MB
`HG00418_A_1.fastq.gz`	Human (1000 Genomes sample HG00418), reads mapping to chromosome 21 - forward reads	Illumina	paired-end (forward)	`fastqsanger.gz`	88 MB
`HG00418_A_2.fastq.gz`	Human (1000 Genomes sample HG00418), reads mapping to chromosome 21 - reverse reads	Illumina	paired-end (reverse)	`fastqsanger.gz`	88 MB
`GOS1.fastq.gz`	Escherichia coli, German outbreak 2011	454	single-end	`fastqsanger.gz`	46 MB
`iontorrent.fastq.gz`	Escherichia coli, German outbreak 2011	Ion Torrent	single-end	`fastqsanger.gz`	101 MB

Galaxy paired collection HG00418: forward = HG00418_A_1.fastq.gz, reverse = HG00418_A_2.fastq.gz.

SHA-256 checksums

Use these to check that a downloaded file is complete and unchanged (shasum -a 256 <file> on macOS/Linux, certutil -hashfile <file> SHA256 on Windows).

File	SHA-256
`Paeruginosa.fastq.gz`	`6a8107c285d404bc6b887e5151bee91f0f2039ec72fac21b18b39f95fc5f8fb0`
`HG00418_A_1.fastq.gz`	`8791ff8e02ef9b73f06331a6277b6de6ed1b49272840af5f0f896f377ffcfb39`
`HG00418_A_2.fastq.gz`	`a9b802798dd50fb4ee38f0a94d34fdb59d6fd5db521a0a4672716fe3fc342f67`
`GOS1.fastq.gz`	`08e4d5a727ae9416fa1bbbf03d8466fe30802cb8a1a0b9f2f20492a87875f4d5`
`iontorrent.fastq.gz`	`7aa88bd0f288d6f1811c7a73b61dd2f3dae2887bc0635035abdc73c1da6eb03d`

Terms of use: Redistribution terms are being confirmed by the instructors. Use the files for this course only.