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dipspades - diploid genome assembler

DIPSPADES(1)   DIPSPADES(1)

NAME

dipspades - diploid genome assembler

SYNOPSIS

dipspades [options] -o <output_dir>

DESCRIPTION

dipspades is the main executable for the dipSPAdes software, a genome assembler designed for diploid genomes with a high heterozygosity rate. 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)
 
--iontorrent
this flag is required for IonTorrent data
 
--test
runs dipSPAdes 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

Input haplocontigs

--hap <filename>
file with haplocontigs

Pipeline options

--only-assembler
runs only assembling (without read error correction)
 
--disable-gzip-output
forces error correction not to compress the corrected reads
 
--disable-rr
disables repeat resolution stage of assembling

dipSPAdes options

--expect-gaps
indicates that significant number of gaps in coverage is expected
 
--expect-rearrangements
indicates that significant number of rearrangements between haplomes of diploid genome is expected
 
--hap-assembly
enables haplotype assembly phase

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]