| faSomeRecords |
faSomeRecords in.fa listFile out.fa |
Extract multiple fasta records |
| vdb-validate |
vdb-validate [options] <path/file> [<path/file> ...] |
Validate the integrity of downloaded SRA data |
| sam-dump |
sam-dump [options] <path/file> [<path/file> ...] |
Convert SRA data to sam format |
| 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 |
| prefetch |
prefetch [options] <path/SRA file | path/kart file> [<path/file> ...] |
Download SRA, dbGaP, and ADSP data from NCBI |
| vdb-config |
vdb-config [options] [<query>] |
Display and modify VDB configuration information |
| illumina-dump |
illumina-dump [options] <path/file> [<path/file> ...] |
Convert SRA data into Illumina native formats (qseq, etc.) |
| fastq-dump |
fastq-dump [options] <accession> |
This tool extracts reads from SRA archives |
| sff-dump |
sff-dump [options] <path/file> [<path/file> ...] |
Convert SRA data to sff format |
| vdb-decrypt |
vdb-decrypt [options] <directory> |
Decrypt non-SRA dbGaP data ("phenotype data") |
| abi-dump |
abi-dump [options] <path/file> [<path/file> ...] |
Convert SRA data into ABI format (csfasta / qual) |
| vdb-decrypt |
vdb-decrypt [options] <source-file> <destination-directory> |
Decrypt non-SRA dbGaP data ("phenotype data") |
| vdb-validate |
vdb-validate [options] <accession> |
Validate the integrity of downloaded SRA data |
| wget |
wget [option]... [URL]... |
The non-interactive network downloader |
| sff-dump |
sff-dump [options] <accession> |
Convert SRA data to sff format |
| prefetch |
prefetch [options] --list <kart_file> |
Download SRA, dbGaP, and ADSP data from NCBI |
| sra-pileup |
sra-pileup [options] <accession> |
Generate pileup statistics on aligned SRA data |
| illumina-dump |
illumina-dump [options] <accession> |
Convert SRA data into Illumina native formats (qseq, etc.) |
| sam-dump |
sam-dump [options] <accession> |
Convert SRA data to sam format |
| sra-pileup |
sra-pileup [options] <path/file> [<path/file> ...] |
Generate pileup statistics on aligned SRA data |