Sra-tools

To load

module load sra-tools

fastq-dump

the chief command for this toolbox is fastq-dump, which downloads the SRA you are looking for

Identifying the right SRA name is an issue, so it's good to be able to do a quick test to see if you have the name correct via

fastq-dump - X 5 -Z SRR390728

"-X 5" just downloads the first five reads, while "-Z" send them to STDOUT. If this doesn't return an error you can go ahead and download via

fastq-dump --split-files SRR390728

The "--split-files" option is for getting pair-ended reads in separate files, but in single-end files, it actually seems to produce the same file under "1" and "_2" suffixes.

"--help" option output

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

INPUT
  -A|--accession <accession>       Replaces accession derived from <path> in 
                                   filename(s) and deflines (only for single 
                                   table dump) 
  --table <table-name>             Table name within cSRA object, default is 
                                   "SEQUENCE" 

PROCESSING

Read Splitting                     Sequence data may be used in raw form or
                                     split into individual reads
  --split-spot                     Split spots into individual reads 

Full Spot Filters                  Applied to the full spot independently
                                     of --split-spot
  -N|--minSpotId <rowid>           Minimum spot id 
  -X|--maxSpotId <rowid>           Maximum spot id 
  --spot-groups <[list]>           Filter by SPOT_GROUP (member): name[,...] 
  -W|--clip                        Apply left and right clips 

Common Filters                     Applied to spots when --split-spot is not
                                     set, otherwise - to individual reads
  -M|--minReadLen <len>            Filter by sequence length >= <len> 
  -R|--read-filter <[filter]>      Split into files by READ_FILTER value 
                                   optionally filter by value: 
                                   pass|reject|criteria|redacted 
  -E|--qual-filter                 Filter used in early 1000 Genomes data: no 
                                   sequences starting or ending with >= 10N 
  --qual-filter-1                  Filter used in current 1000 Genomes data 

Filters based on alignments        Filters are active when alignment
                                     data are present
  --aligned                        Dump only aligned sequences 
  --unaligned                      Dump only unaligned sequences 
  --aligned-region <name[:from-to]>  Filter by position on genome. Name can 
                                   either be accession.version (ex: 
                                   NC_000001.10) or file specific name (ex: 
                                   "chr1" or "1"). "from" and "to" are 1-based 
                                   coordinates 
  --matepair-distance <from-to|unknown>  Filter by distance beiween matepairs. 
                                   Use "unknown" to find matepairs split 
                                   between the references. Use from-to to limit 
                                   matepair distance on the same reference 

Filters for individual reads       Applied only with --split-spot set
  --skip-technical                 Dump only biological reads 

OUTPUT
  -O|--outdir <path>               Output directory, default is working 
                                   directory '.' ) 
  -Z|--stdout                      Output to stdout, all split data become 
                                   joined into single stream 
  --gzip                           Compress output using gzip 
  --bzip2                          Compress output using bzip2 

Multiple File Options              Setting these options will produce more
                                     than 1 file, each of which will be suffixed
                                     according to splitting criteria.
  --split-files                    Dump each read into separate file.Files 
                                   will receive suffix corresponding to read 
                                   number 
  --split-3                        Legacy 3-file splitting for mate-pairs: 
                                   First biological reads satisfying dumping 
                                   conditions are placed in files *_1.fastq and 
                                   *_2.fastq If only one biological read is 
                                   present it is placed in *.fastq Biological 
                                   reads and above are ignored. 
  -G|--spot-group                  Split into files by SPOT_GROUP (member name) 
  -R|--read-filter <[filter]>      Split into files by READ_FILTER value 
                                   optionally filter by value: 
                                   pass|reject|criteria|redacted 
  -T|--group-in-dirs               Split into subdirectories instead of files 
  -K|--keep-empty-files            Do not delete empty files 

FORMATTING

Sequence
  -C|--dumpcs <[cskey]>            Formats sequence using color space (default 
                                   for SOLiD),"cskey" may be specified for 
                                   translation 
  -B|--dumpbase                    Formats sequence using base space (default 
                                   for other than SOLiD). 

Quality
  -Q|--offset <integer>            Offset to use for quality conversion, 
                                   default is 33 
  --fasta <[line width]>           FASTA only, no qualities, optional line 
                                   wrap width (set to zero for no wrapping) 
  --suppress-qual-for-cskey        supress quality-value for cskey 

Defline
  -F|--origfmt                     Defline contains only original sequence name 
  -I|--readids                     Append read id after spot id as 
                                   'accession.spot.readid' on defline 
  --helicos                        Helicos style defline 
  --defline-seq <fmt>              Defline format specification for sequence. 
  --defline-qual <fmt>             Defline format specification for quality. 
                                   <fmt> is string of characters and/or 
                                   variables. The variables can be one of: $ac 
                                   - accession, $si spot id, $sn spot 
                                   name, $sg spot group (barcode), $sl spot 
                                   length in bases, $ri read number, $rn 
                                   read name, $rl read length in bases. '[]' 
                                   could be used for an optional output: if 
                                   all vars in [] yield empty values whole 
                                   group is not printed. Empty value is empty 
                                   string or for numeric variables. Ex: 
                                   @$sn[_$rn]/$ri '_$rn' is omitted if name 
                                   is empty
 
OTHER:
  --disable-multithreading         disable multithreading 
  -h|--help                        Output brief explanation of program usage 
  -V|--version                     Display the version of the program 
  -L|--log-level <level>           Logging level as number or enum string One 
                                   of (fatal|sys|int|err|warn|info) or (0-5) 
                                   Current/default is warn 
  -v|--verbose                     Increase the verbosity level of the program 
                                   Use multiple times for more verbosity 
  --ncbi_error_report              Control program execution environment 
                                   report generation (if implemented). One of 
                                   (never|error|always). Default is error 
  --legacy-report                  use legacy style 'Written spots' for tool 

fastq-dump : 2.5.8 ( 2.5.8-1 )