Fetch Data

Function: Download SRA, dbGaP, and ADSP data from NCBI

Usage: prefetch [options] <SRA accession>

Function: Validate the integrity of downloaded SRA data

Usage: vdb-validate [options] <accession>

Function: The non-interactive network downloader

Usage: wget [option]... [URL]...

Function: Generate pileup statistics on aligned SRA data

Usage: sra-pileup [options] <path/file> [<path/file> ...]

Function: Generate pileup statistics on aligned SRA data

Usage: sra-pileup [options] <accession>

Function: Download SRA, dbGaP, and ADSP data from NCBI

Usage: prefetch [options] --list <kart_file>

Function: Convert SRA data into Illumina native formats (qseq, etc.)

Usage: illumina-dump [options] <accession>

Function: Split a bed up into individual beds (one for each internal exon).

Usage: bedToExons originalBeds.bed splitBeds.bed

Function: Decrypt non-SRA dbGaP data ("phenotype data")

Usage: vdb-decrypt [options] <source-file> <destination-file>

Function: Generate statistics about SRA data (quality distribution, etc.)

Usage: sra-stat [options] <path/file> [<path/file> ...]

Function: This tool extracts reads from SRA archives.

Usage: fastq-dump [options] <path/file> [<path/file> ...]

Function: Fetch wiggle data from UCSC Genome Browser's database or a wig file

Usage: hgWiggle [options] <track names ...>

Function: Output the native VDB format of SRA data.

Usage: vdb-dump [options] <accession>

Function: Encrypt non-SRA dbGaP data ("phenotype data")

Usage: vdb-encrypt [options] <source-file> <destination-file>

Function: Convert SRA data into ABI format (csfasta / qual)

Usage: abi-dump [options] <accession>