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Software Parameter Function More
vdb-config vdb-config [options] [<query>] Display and modify VDB configuration information Show
prefetch prefetch [options] <path/SRA file | path/kart file> [<path/file> ...] Allows command-line downloading of SRA, dbGaP, and ADSP data Show
fastq-dump fastq-dump [options] <accession> This tool extracts reads from SRA archives Show
vdb-decrypt vdb-decrypt [options] <source-file> Decrypt non-SRA dbGaP data ("phenotype data"). vdb-decrypt - decrypt a file or all the files (recursively) in a directory Show
abi-dump abi-dump [options] <path/file> [<path/file> ...] Convert SRA data into ABI format (csfasta / qual) Show
sra-pileup sra-pileup [options] <accession> Generate pileup statistics on aligned SRA data Show
vdb-decrypt vdb-decrypt [options] <source-file> <destination-directory> Decrypt non-SRA dbGaP data ("phenotype data") Show
vdb-decrypt vdb-decrypt [options] <directory> Decrypt non-SRA dbGaP data ("phenotype data") Show
vdb-decrypt vdb-decrypt [options] <source-file> <destination-file> Decrypt non-SRA dbGaP data ("phenotype data") Show
sff-dump sff-dump [options] <path/file> [<path/file> ...] Convert SRA data to sff format Show
illumina-dump illumina-dump [options] <accession> Convert SRA data into Illumina native formats (qseq, etc.) Show
sff-dump sff-dump [options] <accession> Convert SRA data to sff format Show
prefetch prefetch [options] --list <kart_file> Allows command-line downloading of SRA, dbGaP, and ADSP data Show
prefetch prefetch [options] <SRA accession> Allows command-line downloading of SRA, dbGaP, and ADSP data Show
illumina-dump illumina-dump [options] <path/file> [<path/file> ...] Convert SRA data into Illumina native formats (qseq, etc.) Show
sra-pileup sra-pileup [options] <path/file> [<path/file> ...] Generate pileup statistics on aligned SRA data Show
vdb-validate vdb-validate [options] <accession> Validate the integrity of downloaded SRA data Show
sam-dump sam-dump [options] <path/file> [<path/file> ...] Convert SRA data to sam format Show
abi-dump abi-dump [options] <accession> Convert SRA data into ABI format (csfasta / qual) Show
fastq-dump fastq-dump [options] <path/file> [<path/file> ...] This tool extracts reads from SRA archives. Show