SPAdes

SPAdes genome assembler v3.12.0

Usage: /usr/local/bin/SPAdes-3.12.0-Linux/bin/spades.py [options] -o <output_dir>

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>  file with interlaced reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-1 <filename>  file with forward reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-2 <filename>  file with reverse reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-s <filename>  file with unpaired reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-m <filename>  file with merged reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-<or>  orientation of reads for paired-end library number <#> (<#> = 1,2,...,9; <or> = fr, rf, ff)
--s<#>    <filename>  file with unpaired reads for single reads library number <#> (<#> = 1,2,...,9)
--mp<#>-12  <filename>  file with interlaced reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-1 <filename>  file with forward reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-2 <filename>  file with reverse reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-s <filename>  file with unpaired reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-<or>  orientation of reads for mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--hqmp<#>-12  <filename>  file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-1 <filename>  file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-2 <filename>  file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-s <filename>  file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-<or>  orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--nxmate<#>-1 <filename>  file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--nxmate<#>-2 <filename>  file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--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 ('ec', 'as', 'k<int>', 'mc', 'last')
--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]