table of contents
- stretch 3.9.1+dfsg-1
- stretch-backports 3.12.0+dfsg-1~bpo9+1
DIPSPADES(1) | DIPSPADES(1) |
NAME¶
dipspades - diploid genome assemblerSYNOPSIS¶
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>--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>
Input haplocontigs¶
--hap <filename>Pipeline options¶
--only-assembler--disable-gzip-output
--disable-rr
dipSPAdes options¶
--expect-gaps--expect-rearrangements
--hap-assembly
Advanced options¶
--dataset <filename>-t/--threads <int>
-m/--memory <int>
--tmp-dir <dirname>
-k <int,int,...>
--cov-cutoff <float>
--phred-offset <33 or 64>