Fetch Data

vdb-validate
Function: Validate the integrity of downloaded SRA data
Usage: vdb-validate [options] <path/file> [<path/file> ...]
faSomeRecords
Function: Extract multiple fasta records
Usage: faSomeRecords in.fa listFile out.fa
sam-dump
Function: Convert SRA data to sam format
Usage: sam-dump [options] <path/file> [<path/file> ...]
fetchChromSizes
Function: Fetch chrom.sizes information from UCSC for the given <db>
Usage: fetchChromSizes <db> > <db>.chrom.sizes
vdb-config
Function: Display and modify VDB configuration information
Usage: vdb-config [options] [<query>]
prefetch
Function: Download SRA, dbGaP, and ADSP data from NCBI
Usage: prefetch [options] <path/SRA file | path/kart file> [<path/file> ...]
vdb-decrypt
Function: Decrypt non-SRA dbGaP data ("phenotype data"). vdb-decrypt - decrypt a file or all the files (recursively) in a directory
Usage: vdb-decrypt [options] <source-file>
illumina-dump
Function: Convert SRA data into Illumina native formats (qseq, etc.)
Usage: illumina-dump [options] <path/file> [<path/file> ...]
fastq-dump
Function: This tool extracts reads from SRA archives
Usage: fastq-dump [options] <accession>
sff-dump
Function: Convert SRA data to sff format
Usage: sff-dump [options] <path/file> [<path/file> ...]
sam-dump
Function: Convert SRA data to sam format
Usage: sam-dump [options] <accession>
vdb-decrypt
Function: Decrypt non-SRA dbGaP data ("phenotype data")
Usage: vdb-decrypt [options] <directory>
vdb-decrypt
Function: Decrypt non-SRA dbGaP data ("phenotype data")
Usage: vdb-decrypt [options] <source-file> <destination-directory>
sff-dump
Function: Convert SRA data to sff format
Usage: sff-dump [options] <accession>
abi-dump
Function: Convert SRA data into ABI format (csfasta / qual)
Usage: abi-dump [options] <path/file> [<path/file> ...]