Utility Python package to download Genome-in-a-Bottle data from their index files.
Project description
download_giab
Utility Python package to download Genome-in-a-Bottle (GIAB) data from their index files.
This requires Python 3.6 or later.
To install, run the following:
pip install download_giab
If you're installing on a cluster, this might be more like:
pip install --user download_giab
To use, run something like the following:
download_giab https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002
This will download everything in the linked index to the directory the utility is run from. It can also download from local index files.
If you want to download lots of data and not have the program hang up upon session disconnect,
you can use nohup
and &
:
nohup download_giab https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 &
If you are downloading paired-end reads and want to concatenate all FASTQ files into two files,
you can use the --cat-paired
flag. This will generate two files per sample: [sample]_1.fastq.gz
and [sample]_2.fastq.gz
. If a sample ID is not present, the literal text paired
will be used.
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