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]