table of contents
- stretch 3.9.1+dfsg-1
- testing 3.13.0+dfsg2-2
- stretch-backports 3.12.0+dfsg-1~bpo9+1
- unstable 3.13.0+dfsg2-2
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>--sc
--meta
--rna
--plasmid
--iontorrent
--test
-h/--help
Input data¶
--12 <filename>-1 <filename>
-2 <filename>
-s <filename>
--pe<#>-12 <filename>
--pe<#>-1 <filename>
--pe<#>-2 <filename>
--pe<#>-s <filename>
--pe<#>-<or>
--s<#> <filename>
--mp<#>-12 <filename>
--mp<#>-1 <filename>
--mp<#>-2 <filename>
--mp<#>-s <filename>
--mp<#>-<or>
--hqmp<#>-12 <filename>
--hqmp<#>-1 <filename>
--hqmp<#>-2 <filename>
--hqmp<#>-s <filename>
--hqmp<#>-<or>
--nxmate<#>-1 <filename>
--nxmate<#>-2 <filename>
--sanger <filename>
--pacbio <filename>
--nanopore <filename>
--trusted-contigs <filename>
--untrusted-contigs <filename>
Pipeline options¶
--only-error-correction--only-assembler
--careful
--continue
--restart-from <cp>
--disable-gzip-output
--disable-rr
Advanced options¶
--dataset <filename>-t/--threads <int>
-m/--memory <int>
--tmp-dir <dirname>
-k <int,int,...>
--cov-cutoff <float>
--phred-offset <33 or 64>