Data

When running bioinformatics analyses on the command-line, you may wish to use publicly-available data for testing or for analysis. Some examples of how to do this are given here, along with sample datasets.

Get data with wget or curl

At the command line, type:

• wget [address of file] or
• curl -o [give the file a name][address of file]

More about wget: https://en.wikipedia.org/wiki/Wget

More about curl: https://en.wikipedia.org/wiki/CURL

SRA Toolkit

• Find some SRR numbers for reads you are interested in (search NCBI’s SRA)
• At the command line, type fastq-dump SRR[number goes here]
• Note: the SRR numbers refer to the sequencing run. https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/
• Note: fasterq-dump is now also supported and fastq-dump may be deprecated in the future.
• More about the SRA Toolkit: https://github.com/ncbi/sra-tools/wiki

Sample sequencing data

PacBio reads From Canu’s quickstart page:

• curl -L -o pacbio.fastq \ http://gembox.cbcb.umd.edu/mhap/raw/ecoli_p6_25x.filtered.fastq

Synthetic PacBio data

• wget https://zenodo.org/record/1009308/files/pacbio.fq?download=1

Nanopore reads From Canu’s quickstart page; data from the Loman lab:

• curl -L -o oxford.fasta \ http://nanopore.s3.climb.ac.uk/MAP006-PCR-1_2D_pass.fasta

Downsampled nanopore data

• wget \ https://zenodo.org/record/842795/files/minion_1.2d_pass.fastq.fastqsanger?download=1

fast5 files

• https://figshare.com/articles/Raw_ONT_reads_-_barcode_1/5353210

10X (linked) reads

• https://www.10xgenomics.com/resources/datasets/