SPAdes command line options

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SPAdes command line options

Option	Argument	Description
Basic options
-o	<output_dir>	Directory to store all the resulting files (required)
–sc		This flag is required for MDA (single-cell) data
–meta		This flag is required for metagenomic sample data
–rna		This flag is required for RNA-Seq data
–plasmid		Runs plasmidSPAdes pipeline for plasmid detection
–iontorrent		This flag is required for IonTorrent data
–test		Runs SPAdes on toy dataset
-h/–help		Prints this usage message
-v/–version		Prints version
Input data
–12	<filename>	File with interlaced forward and reverse paired-end reads
-1	<filename>	File with forward paired-end reads
-2	<filename>	File with reverse paired-end reads
-s	<filename>	File with unpaired reads
–merged	<filename>	File with merged forward and reverse paired-end reads
–pe<#>-12	<filename>	Interlaced reads for paired-end library number
–pe<#>-1	<filename>	Forward reads for paired-end library number
–pe<#>-2	<filename>	Reverse reads for paired-end library number
–pe<#>-s	<filename>	Unpaired reads for paired-end library number
–pe<#>-m	<filename>	Merged reads for paired-end library number
–pe<#>-	<orientation>	Orientation of reads for paired-end library number
–s<#>	<filename>	File with unpaired reads for single reads library number
–mp<#>-12	<filename>	Interlaced reads for mate-pair library number
–mp<#>-1	<filename>	Forward reads for mate-pair library number
–mp<#>-2	<filename>	Reverse reads for mate-pair library number
–mp<#>-s	<filename>	Unpaired reads for mate-pair library number
–mp<#>-	<orientation>	Orientation of reads for mate-pair library number
–hqmp<#>-12	<filename>	Interlaced reads for high-quality mate-pair library number
–hqmp<#>-1	<filename>	Forward reads for high-quality mate-pair library number
–hqmp<#>-2	<filename>	Reverse reads for high-quality mate-pair library number
–hqmp<#>-s	<filename>	Unpaired reads for high-quality mate-pair library number
–hqmp<#>-	<orientation>	Orientation of reads for high-quality mate-pair library number
–nxmate<#>-1	<filename>	Forward reads for Lucigen NxMate library number
–nxmate<#>-2	<filename>	Reverse reads for Lucigen NxMate library number
–sanger	<filename>	File with Sanger reads
–pacbio	<filename>	File with PacBio reads
–nanopore	<filename>	File with Nanopore reads
–tslr	<filename>	File with TSLR-contigs
–trusted-contigs	<filename>	File with trusted contigs
–untrusted-contigs	<filename>	File with untrusted contigs
Pipeline options
–only-error-correction		Runs only read error correction (without assembling)
–only-assembler		Runs only assembling (without read error correction)
–careful		Tries to reduce number of mismatches and short indels
–continue		Continue run from the last available check-point
–restart-from	<cp>	Restart run with updated options and from the specified check-point
–disable-gzip-output		Forces error correction not to compress the corrected reads
–disable-rr		Disables repeat resolution stage of assembling
Advanced options
–dataset	<filename>	File with dataset description in YAML format
-t/–threads	<int>	Number of threads [default: 16]
-m/–memory	<int>	RAM limit for SPAdes in Gb [default: 250]
–tmp-dir	<dirname>	Directory for temporary files [default: /tmp]
-k	<int,int,...>	Comma-separated list of k-mer sizes [default: ‘auto’]
–cov-cutoff	<float>	Coverage cutoff value [default: ‘off’]
–phred-offset	<33 or 64>	PHRED quality offset in the input reads [default: auto-detect]

Performance Recommendations

[x] Use --careful for improved accuracy [x] Adjust k-mer sizes for different genome complexities [x] Monitor memory usage with --memory-limit

SPAdes basic command line usage

spades.py [options] -o <output_dir>

Examples

spades.py -1 SRR27753935_1.fastq -2 SRR27753935_2.fastq \
    -m 32 -t 16 -k 21,33,55 \
    --careful \
    -o spades_results

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References

Feedback and bug reports Please, leave your comments and bug reports at SPAdes GitHub repository tracker.