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SPADES(1) | SPADES(1) |
NAME¶
spades - SPAdes genome assemblerSYNOPSIS¶
spades [options] -o <output_dir>DESCRIPTION¶
spades is the main executable for the SPAdes software. It assembles genomic reads given to it and places the resulting assembly in <output_dir>.OPTIONS¶
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
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
--pe<#>-12 <filename>
file with interlaced reads for paired-end library number
<#> (<#> = 1,2,3,4,5)
--pe<#>-1 <filename>
file with forward reads for paired-end library number
<#> (<#> = 1,2,3,4,5)
--pe<#>-2 <filename>
file with reverse reads for paired-end library number
<#> (<#> = 1,2,3,4,5)
--pe<#>-s <filename>
file with unpaired reads for paired-end library number
<#> (<#> = 1,2,3,4,5)
--pe<#>-<or>
orientation of reads for paired-end library number
<#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
--s<#> <filename>
file with unpaired reads for single reads library number
<#> (<#> = 1,2,3,4,5)
--mp<#>-12 <filename>
file with interlaced reads for mate-pair library number
<#> (<#> = 1,2,3,4,5)
--mp<#>-1 <filename>
file with forward reads for mate-pair library number
<#> (<#> = 1,2,3,4,5)
--mp<#>-2 <filename>
file with reverse reads for mate-pair library number
<#> (<#> = 1,2,3,4,5)
--mp<#>-s <filename>
file with unpaired reads for mate-pair library number
<#> (<#> = 1,2,3,4,5)
--mp<#>-<or>
orientation of reads for mate-pair library number
<#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
--hqmp<#>-12 <filename>
file with interlaced reads for high-quality mate-pair
library number <#> (<#> = 1,2,3,4,5)
--hqmp<#>-1 <filename>
file with forward reads for high-quality mate-pair
library number <#> (<#> = 1,2,3,4,5)
--hqmp<#>-2 <filename>
file with reverse reads for high-quality mate-pair
library number <#> (<#> = 1,2,3,4,5)
--hqmp<#>-s <filename>
file with unpaired reads for high-quality mate-pair
library number <#> (<#> = 1,2,3,4,5)
--hqmp<#>-<or>
orientation of reads for high-quality mate-pair library
number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
--nxmate<#>-1 <filename>
file with forward reads for Lucigen NxMate library number
<#> (<#> = 1,2,3,4,5)
--nxmate<#>-2 <filename>
file with reverse reads for Lucigen NxMate library number
<#> (<#> = 1,2,3,4,5)
--sanger <filename>
file with Sanger reads
--pacbio <filename>
file with PacBio reads
--nanopore <filename>
file with Nanopore reads
--trusted-contigs <filename>
file with trusted contigs
--untrusted-contigs <filename>
file with untrusted contigs
Pipeline options¶
--only-error-correctionruns 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 ('ec', 'as', 'k<int>', 'mc')
--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 (terminates if exceeded)
[default: 250]
--tmp-dir <dirname>
directory for temporary files [default:
<output_dir>/tmp]
-k <int,int,...>
comma-separated list of k-mer sizes (must be odd and less
than 128) [default: 'auto']
--cov-cutoff <float>
coverage cutoff value (a positive float number, or
'auto', or 'off') [default: 'off']
--phred-offset <33 or 64>
PHRED quality offset in the input reads (33 or 64)
[default: auto-detect]