SPAdes-Teaching
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Category
Bioinformatics
Program On
Teaching
Version
3.11.1
Author / Distributor
Description
"Genome assembler for single-cell and isolates data sets" More details are at SPAdes
Running Program
The last version of this application is at /usr/local/apps/eb/SPAdes/3.11.1-foss-2016b
To use this version, please load the module with
ml SPAdes/3.11.1-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_SPAdes
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=SPAdes.%j.out
#SBATCH --error=SPAdes.%j.err
cd $SLURM_SUBMIT_DIR
ml SPAdes/3.11.1-foss-2016b
spades.py [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml SPAdes/3.11.1-foss-2016b
spades.py -h
SPAdes genome assembler v3.11.1
Usage: /usr/local/apps/eb/SPAdes/3.11.1-foss-2016b/bin/spades.py [options] -o <output_dir>
Basic options:
-o <output_dir> directory to store all the resulting files (required)
--sc this flag is required for MDA (single-cell) data
--meta this flag is required for metagenomic sample data
--rna this flag is required for RNA-Seq data
--plasmid runs plasmidSPAdes pipeline for plasmid detection
--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
--pe<#>-12 <filename> file with interlaced reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-1 <filename> file with forward reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-2 <filename> file with reverse reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-s <filename> file with unpaired reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-<or> orientation of reads for paired-end library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--s<#> <filename> file with unpaired reads for single reads library number <#> (<#> = 1,2,..,9)
--mp<#>-12 <filename> file with interlaced reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-1 <filename> file with forward reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-2 <filename> file with reverse reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-s <filename> file with unpaired reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-<or> orientation of reads for mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--hqmp<#>-12 <filename> file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-1 <filename> file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-2 <filename> file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-s <filename> file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-<or> orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--nxmate<#>-1 <filename> file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--nxmate<#>-2 <filename> file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--sanger <filename> file with Sanger reads
--pacbio <filename> file with PacBio reads
--nanopore <filename> file with Nanopore reads
--tslr <filename> file with TSLR-contigs
--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
--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]
Installation
Source code is obtained from SPAdes
System
64-bit Linux