Assembles a small genome (bacterial, fungal, viral)
Input
name:type
description
pattern
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
illumina:file
List of input FastQ (Illumina or PacBio CCS reads) files
of size 1 and 2 for single-end and paired-end data,
respectively. This input data type is required.
pacbio:file
List of input PacBio CLR FastQ files of size 1.
nanopore:file
List of input FastQ files of size 1, originating from Oxford Nanopore technology.
yml:file
Path to yml file containing read information.
The raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) in addition to this YML.
File entries in this yml must contain only the file name and no paths.
*.{yml,yaml}
hmm:file
File or directory with amino acid HMMs for Spades HMM-guided mode.
Output
name:type
description
pattern
scaffolds
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fa.gz
*.scaffolds.fa.gz:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fa.gz
contigs
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fa.gz
*.contigs.fa.gz:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fa.gz
transcripts
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fa.gz
*.transcripts.fa.gz:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fa.gz
gene_clusters
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fa.gz
*.gene_clusters.fa.gz:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fa.gz
gfa
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.gfa.gz
*.assembly.gfa.gz:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.gfa.gz
warnings
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.warnings.log:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
log
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.spades.log
*.spades.log:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.spades.log
versions
versions.yml:file
File containing software versions
versions.yml
Tools
spades
GPL v2
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
