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= fr, rf, ff)sZ--s<#> file with unpaired reads for single reads library number <#> (<#> = %s)Rsb--mp<#>-12 file with interlaced reads for mate-pair library number <#> (<#> = 1,2,..,9)s^--mp<#>-1 file with forward reads for mate-pair library number <#> (<#> = 1,2,..,9)s^--mp<#>-2 file with reverse reads for mate-pair library number <#> (<#> = 1,2,..,9)s_--mp<#>-s file with unpaired reads for mate-pair library number <#> (<#> = 1,2,..,9)sf--mp<#>- orientation of reads for mate-pair library number <#> (<#> = 1,2,..,9; = fr, rf, ff)sq--hqmp<#>-12 file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)sm--hqmp<#>-1 file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)sm--hqmp<#>-2 file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)sn--hqmp<#>-s file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)su--hqmp<#>- orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9; = fr, rf, ff)sg--nxmate<#>-1 file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)sg--nxmate<#>-2 file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)s+--sanger file with Sanger reads s+--pacbio file with PacBio reads s/--nanopore file with Nanopore reads s)--tslr file with TSLR-contigs s7--trusted-contigs file with trusted contigs s;--untrusted-contigs file with untrusted contigs sJ--ss- strand specific data, = fr (normal) and rf (antisense) sPipeline options:sL--only-error-correction runs only read error correction (without assembling)sE--only-assembler runs only assembling (without read error correction)s@--careful tries to reduce number of mismatches and short indelss<--continue continue run from the last available check-pointsl--restart-from restart run with updated options and from the specified check-point ('ec', 'as', 'last')s|--restart-from restart run with updated options and from the specified check-point ('ec', 'as', 'k', 'mc', 'last')sQ--disable-gzip-output forces error correction not to compress the corrected readss<--disable-rr disables repeat resolution stage of assemblingsAdvanced options:sA--dataset file with dataset description in YAML formatsU--fast speeds up isoform detection, but may miss short and low-expressed isoforms s%-t/--threads number of threadss [default: %s] sF-m/--memory RAM limit for SPAdes in Gb (terminates if exceeded)s1--tmp-dir directory for temporary filess [default: /tmp]sF-k comma-separated list of k-mer sizes (must be odd ands less than is) [default: 'auto']s1-k k-mer size (must be odd and less than s) [default: 'auto'] sk--cov-cutoff coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']sL--phred-offset <33 or 64> PHRED quality offset in the input reads (33 or 64)s [default: auto-detect]sHIDDEN options:s@--debug runs SPAdes in debug mode (keeps intermediate output)sd--stop-after runs SPAdes until the specified check-point ('ec', 'as', 'k', 'mc') inclusives&--truseq runs SPAdes in TruSeq mode sU--mismatch-correction runs post processing correction of mismatches and short indelssQ--reference file with reference for deep analysis (only in debug mode)sP--series-analysis config for metagenomics-series-augmented reassemblys2--configs-dir directory with configssT-i/--iterations number of iterations for read error correction [default: %s] sI--read-buffer-size sets size of read buffer for graph constructionsL--bh-heap-check sets HEAPCHECK environment variable for BayesHammersJ--spades-heap-check sets HEAPCHECK environment variable for SPAdess8--large-genome Enables optimizations for large genomes sU--save-gp Enables saving graph pack before repeat resolution (even without --debug) sª--hidden-cov-cutoff coverage cutoff value deeply integrated in simplification (a positive float number). 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