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]