# SPAdes 3.15.3


## SPAdes – St. Petersburg genome assembler

SPAdes is an assembly toolkit containing various assembly pipelines

Location and version:

```console
$ which spades.py
/local/cluster/SPAdes/bin/spades.py
$ spades.py --version
SPAdes genome assembler v3.15.3
```

help message:

```console
$ spades.py --help
SPAdes genome assembler v3.15.3

Usage: spades.py [options] -o <output_dir>

Basic options:
  -o <output_dir>             directory to store all the resulting files (required)
  --isolate                   this flag is highly recommended for high-coverage isolate and multi-cell data
  --sc                        this flag is required for MDA (single-cell) data
  --meta                      this flag is required for metagenomic data
  --bio                       this flag is required for biosyntheticSPAdes mode
  --corona                    this flag is required for coronaSPAdes mode
  --rna                       this flag is required for RNA-Seq data
  --plasmid                   runs plasmidSPAdes pipeline for plasmid detection
  --metaviral                 runs metaviralSPAdes pipeline for virus detection
  --metaplasmid               runs metaplasmidSPAdes pipeline for plasmid detection in metagenomic datasets (equivalent for --meta --plasmid)
  --rnaviral                  this flag enables virus assembly module from RNA-Seqdata
  --iontorrent                this flag is required for IonTorrent data
  --test                      runs SPAdes on toy dataset
  -h, --help                  prints this usage message
  -v, --version               prints version

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
  --merged <filename>         file with merged forward and reverse paired-end reads
  --pe-12 <#> <filename>      file with interlaced reads for paired-end library number <#>.
                              Older deprecated syntax is -pe<#>-12 <filename>
  --pe-1 <#> <filename>       file with forward reads for paired-end library number <#>.
                              Older deprecated syntax is -pe<#>-1 <filename>
  --pe-2 <#> <filename>       file with reverse reads for paired-end library number <#>.
                              Older deprecated syntax is -pe<#>-2 <filename>
  --pe-s <#> <filename>       file with unpaired reads for paired-end library number <#>.
                              Older deprecated syntax is -pe<#>-s <filename>
  --pe-m <#> <filename>       file with merged reads for paired-end library number<#>.
                              Older deprecated syntax is -pe<#>-m <filename>
  --pe-or <#> <or>            orientation of reads for paired-end library number <#>
                              (<or> = fr, rf, ff).
                              Older deprecated syntax is -pe<#>-<or>
  --s <#> <filename>          file with unpaired reads for single reads library number <#>.
                              Older deprecated syntax is --s<#> <filename>
  --mp-12 <#> <filename>      file with interlaced reads for mate-pair library number <#>.
                              Older deprecated syntax is -mp<#>-12 <filename>
  --mp-1 <#> <filename>       file with forward reads for mate-pair library number<#>.
                              Older deprecated syntax is -mp<#>-1 <filename>
  --mp-2 <#> <filename>       file with reverse reads for mate-pair library number<#>.
                              Older deprecated syntax is -mp<#>-2 <filename>
  --mp-s <#> <filename>       file with unpaired reads for mate-pair library number <#>.
                              Older deprecated syntax is -mp<#>-s <filename>
  --mp-or <#> <or>            orientation of reads for mate-pair library number <#>

                              (<or> = fr, rf, ff).
                              Older deprecated syntax is -mp<#>-<or>
  --hqmp-12 <#> <filename>    file with interlaced reads for high-quality mate-pair library number <#>.
                              Older deprecated syntax is -hqmp<#>-12 <filename>
  --hqmp-1 <#> <filename>     file with forward reads for high-quality mate-pair library number <#>.
                              Older deprecated syntax is -hqmp<#>-1 <filename>
  --hqmp-2 <#> <filename>     file with reverse reads for high-quality mate-pair library number <#>.
                              Older deprecated syntax is -hqmp<#>-2 <filename>
  --hqmp-s <#> <filename>     file with unpaired reads for high-quality mate-pair library number <#>.
                              Older deprecated syntax is -hqmp<#>-s <filename>
  --hqmp-or <#> <or>          orientation of reads for high-quality mate-pair library number <#>
                              (<or> = fr, rf, ff).
                              Older deprecated syntax is -hqmp<#>-<or>
  --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

Pipeline options:
  --only-error-correction     runs only read error correction (without assembling)
  --only-assembler            runs only assembling (without read error correction)
  --careful                   tries to reduce number of mismatches and short indels
  --checkpoints <last or all>
                              save intermediate check-points ('last', 'all')
  --continue                  continue run from the last available check-point (only -o should be specified)
  --restart-from <cp>         restart run with updated options and from the specified check-point
                              ('ec', 'as', 'k<int>', 'mc', 'last')
  --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 <int>, --threads <int>   number of threads. [default: 16]
  -m <int>, --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> ...]        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]
  --custom-hmms <dirname>     directory with custom hmms that replace default ones,
                              [default: None]
```

SPAdes is an exceptional assembler, especially for prokaryotic organisms and
using illumina short reads.

We recommend using the `--careful` flag. If you plan on assembling many genomes
at once, ensure that you read/write to a local `/data` directory.

software ref: <https://github.com/ablab/spades>  
software ref: <https://cab.spbu.ru/software/spades>  
research ref: <https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.102>