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]