Page Comparison

cds-mapping-stats  metaplasmidspades.py  rnaspades.py                 spades-gbuilder       spades.py                 truspades.py
cds-subgraphs      metaspades.py         rnaviralspades.py            spades-gmapper        spades-read-filter                    
coronaspades.py    metaviralspades.py    spades-bwa                   spades-gsimplifier    spades-kmer-estimating                
mag-improve        plasmidspades.py      spades-convert-bin-to-fasta  spades-kmercount      spaligner                       

[salexan5@tlog2 2.1.1]$ spades.py --help
SPAdes genome assembler v3.15.2

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-Seq data
  --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-bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.16a-r1181
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.

...
#SBATCH --cpus-per-task=8
#SBATCH --mem=60G
...
module load gcc/7.3.0 spades/3.15.2-py27
...
spades.py -t 8 -m 60 ...