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

versions (file)

File containing software versions

versions.yml

meta (map)

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

]

fastq (file)

Simulated reads

*.fq.gz

aln (file)

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

*.aln

sam (file)

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

*.sam
included in
readsimulator
maintainer
Github user MarieLataretu
get in touch
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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