fastq-dump options

Not all the options available to fastq-dump are listed on the NCBI website. It is not a very well documented program! Here is the current list.

Here is the list of options on the NCBI fastq-dump website. Note at the bottom that it states this is forĀ fastq-dump v2.5x


Here is a list of options from fastq-dump 2.5.5:

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

 -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 


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: 
 -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 
 --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

 -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 
 --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: 
 -T|--group-in-dirs Split into subdirectories instead of files 
 -K|--keep-empty-files Do not delete empty files


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

 -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

 -F|--origfmt Defline contains only original sequence name 
 -I|--readids Append read id after spot id as 
 '' 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
 --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 : 2.5.5