modules/art_illumina

Simulation tool to generate synthetic Illumina next-generation sequencing reads

fastqfastailluminasimulate

https://github.com/nf-core/modules/[...]/modules/nf-core/art/illumina

Description

Simulation tool to generate synthetic Illumina next-generation sequencing reads

Input

name:type

description

pattern

`meta:map`

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

`fasta:file`

FASTA file of input DNA/RNA reference

*.{fasta,fa}

`sequencing_system:string`

The name of Illumina sequencing system of the built-in profile used for simulation

`fold_coverage:integer`

The fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon

`read_length:integer`

The length of reads to be simulated

Output

name:type

description

pattern

`fastq`

`meta:map`

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

`*.fq.gz:file`

Simulated reads

*.fq.gz

`aln`

`meta:map`

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

`*.aln:file`

OPTIONAL Alignment file of the simulated reads. Enabled by default, to disable, use -na/—noALN.

*.aln

`sam`

`meta:map`

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

`*.sam:file`

OPTIONAL Alignment file in SAM format of the simulated reads. Enabled with -sam/—samout.

*.sam

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

art
GPL version 3 license

ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles.

niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm 10.1093/bioinformatics/btr708

modules/art_illumina

Description

Input

`meta:map`

`fasta:file`

`sequencing_system:string`

`fold_coverage:integer`

`read_length:integer`

Output

`fastq`

`meta:map`

`*.fq.gz:file`

`aln`

`meta:map`

`*.aln:file`

`sam`

`meta:map`

`*.sam:file`

`versions`

`versions.yml:file`

Tools

art
GPL version 3 license

included in

maintainers

get in touch

modules/art_illumina

Description

Input

meta:map

fasta:file

sequencing_system:string

fold_coverage:integer

read_length:integer

Output

fastq

meta:map

*.fq.gz:file

aln

meta:map

*.aln:file

sam

meta:map

*.sam:file

versions

versions.yml:file

Tools

art GPL version 3 license

included in

maintainers

get in touch

`meta:map`

`fasta:file`

`sequencing_system:string`

`fold_coverage:integer`

`read_length:integer`

`fastq`

`meta:map`

`*.fq.gz:file`

`aln`

`meta:map`

`*.aln:file`

`sam`

`meta:map`

`*.sam:file`

`versions`

`versions.yml:file`

art
GPL version 3 license