Description

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

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

scaffolds (file)

Fasta file containing scaffolds

*.fa.gz

contigs (file)

Fasta file containing contigs

*.fa.gz

transcripts (file)

Fasta file containing transcripts

*.fa.gz

gene_clusters (file)

Fasta file containing gene_clusters

*.fa.gz

gfa (file)

gfa file containing assembly

*.gfa.gz

log (file)

Spades log file

*.log

versions (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.