spades¶
Purpose¶
This components assembles paired-end FastQ files using the Spades assembler.
Note
Software page: http://bioinf.spbau.ru/spades
Input/Output type¶
- Input type:
FastQ
- Output type:
Fasta
Note
The default input parameter for FastQ data is --fastq
. You can change
the --fastq
parameter default pattern (fastq/*_{1,2}.*
) according
to input file names (e.g.: --fastq "path/to/fastq/*R{1,2}.*"
).
Parameters¶
spadesMinCoverage
: The minimum number of reads to consider an edge in the de Bruijn graph during the assemblyspadesMinKmerCoverage
: Minimum contigs K-mer coverage. After assembly only keep contigs with reported k-mer coverage equal or above this valuespadesKmers
: If ‘auto’ the SPAdes k-mer lengths will be determined from the maximum read length of each assembly. If ‘default’, SPAdes will use the default k-mer lengths.
Published results¶
results/assembly/spades
: Stores the fasta assemblies for each sample.
Published reports¶
None.
Default directives¶
cpus
: 4memory
: 5GB (dynamically increased on retry)container
: ummidock/spadesversion
: 3.13.0-1scratch
: true