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RNASPADES(1)   RNASPADES(1)

NAME

rnaspades - SPAdes genome assembler (rnaSPAdes mode)

SYNOPSIS

rnaspades [options] -o <output_dir>

DESCRIPTION

rnaspades runs SPAdes in rnaSPAdes mode.

OPTIONS

Basic options

-o <output_dir>
directory to store all the resulting files (required)
--iontorrent
this flag is required for IonTorrent data
--test
runs SPAdes 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)
--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)
--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')
--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]